Nucleic Acid Structure: DNA

• Session 2 focuses on Nucleic Acid Structure, as part of the Level 6 Certificate in Food Science and Technology.
• The learning objectives include defining DNA structure and packing, describing nucleotides, the double helix, histones, and chromosomes, detailing the impact of gene mutations, and describing methods of DNA analysis.
• Module content includes cell structure and function, proteins and analysis, nucleic acids, lipids, carbohydrates, nutrition, enzymes, quantitative analysis, spectro & lambda max, weights, measures and preparation for biology, along with the periodic table, chemical bonds, acids and bases, and elemental analysis for chemistry.

DNA

• DNA serves as the hereditary material of the cell and determines the characteristics of species and individuals (e.g., eye color, baldness predisposition, predisposition to certain diseases like cancer or diabetes).
• DNA characteristics are heritable, passed from one generation to the next.
• DNA enables cells to produce identical daughter cells.
• DNA is organized into chromosomes found in the nucleus (or nucleoid in bacteria).
• Chromosomal DNA's packaging within the nucleus is aided by histone proteins.
• Genes are contained within DNA and provide instructions for making a specific protein.
• The nuclear envelope or nuclear membrane separates the nucleus from the cytosol, featuring two lipid bilayers.
• Nuclear pores are present in both membrane bilayers, allowing substance passage between the cytoplasm and nucleus.
• The nucleoplasm is a gel-like substance resembling cytosol that occupies the space within the nucleus.

Types of Nucleic Acids

• DNA stores and transmits hereditary information.
• RNA is derived from DNA and is used in protein synthesis.
• Genes are composed of DNA and are organized into chromosomes.
• Genes contain step-by-step information to make a specific protein.
• Messenger RNA (mRNA) is used for protein synthesis (transcription) as a copy of a gene carrying genetic information.
• Transfer RNA (tRNA) carries amino acids to the ribosome for translation, playing a key role in protein synthesis.
• Transcription makes RNA copies of genes.
• Translation synthesizes proteins for cellular functions.

Nucleotides

• DNA and RNA are made from nucleotides, which are monomers.
• Nucleotides are of 2 types: purines and pyrimidines.
• Purines have a double-ring nitrogenous base and include adenine (A) and guanine (G).
• Pyrimidines have a single-ring nitrogenous base and include cytosine (C, only in DNA), thymine (T, only in DNA), and uracil (U, only in RNA).
• Nucleotides consist of a phosphate group, a pentose (5-carbon) sugar, and a nitrogenous base.
• DNA contains deoxyribose sugar.
• RNA contains ribose sugar.

DNA Structure

• The DNA double helix was proposed in 1953.
• DNA is a double nucleotide chain held by hydrogen bonds between opposing nucleotide base pairs.
• The two DNA strands in a double helix face in opposite directions.
• The 5' end of one strand pairs with the 3' end of the other strand.
• Pyrimidines exclusively form hydrogen bonds with purines.
• Adenine (A) bonds with thymine (T), and guanine (G) bonds with cytosine (C).
• A bonds with T and G with C due to size constraints in the ring structure.
• Guanine (G) and Adenine (A) have a purine ring structure.
• Cytosine and (C) and Thymine (T) have a pyrimidine ring structure.
• Pyrimidine bonds can't form, as they would be too far apart in the double helix of DNA.
• Adenine (A) is opposite Thymine (T) with two hydrogen bonds.
• Guanine (G) is opposite Cytosine (C) with three hydrogen bonds.
• The haploid human genome contains approximately 3 billion base pairs of DNA packaged into 23 chromosomes.
• With 23 pairs of chromosomes, there are 6 billion base pairs of DNA per cell in diploid cells, such as those in the body, (except for female ova and male sperm).

Chromatin & Histones

• Certain proteins called histones compact the chromosomal DNA, forming a DNA-protein complex called chromatin.
• Histones are small, positively charged proteins that bind to negatively charged DNA due to phosphate groups in its phosphate-sugar backbone.
• The first level of DNA packing is the nucleosome.
• Each nucleosome contains eight histone proteins, with DNA wrapping around the histone to achieve a condensed coiled form.
• Chromatin forms chromosomes, a characteristic formation.
• Each chromosome includes one double-stranded piece of DNA along with histones.
• Chromatin becomes more tightly packed during cell division and is visible with a light microscope.
• Chromatin is less tightly packed in eukaryotic cells not dividing, during interphase.
• The looser configuration permits DNA replication and transcription to occur.
• Prokaryotic DNA is generally a single circular chromosome in the cytoplasm, as prokaryotic cells do not possess a nucleus.
• DNA replication is semi-conservative, resulting in a double helix composed of an old and a new strand.

Genetic Mutation

• A genetic mutation is a change in the DNA sequence potentially leading to incomplete or damaged DNA, as well as genetic disorders or illnesses.
• This can result from the order of base nucleotides and/or a change in one or more nucleotides, in many genes, loss of one or more genes or a rearrangement of genes or whole Chromosomes.
• ATA encodes for Methionine .
• GTA encodes Valine.
• Hereditary mutations include Cystic Fibrosis, Hemophilia, Sickle Cell Anemia and Huntington's diseases when a parent carries a gene mutation in their egg or sperm.
• Skin cancer is an other mutation, happening during a person's life.

DNA Analysis & Separation

• DNA analysis involves techniques like agarose gel electrophoresis.
• During electrophoresis, porous buffer filled gel media is used, and DNA/RNA migrates toward a positive electrode,
• Agarose gel electrophoresis separates DNA as a result of its strong negative charge from phosphate groups.
• Smaller DNA/RNA molecules move faster through the gel's sieving effect.
• A fluorescent stain is used to visualise the DNA bands following separation, binding to the DNA
• Upon UV illumination of the gel, the DNA bands are visualised as fluorescent bands.
• Agarose gel electrophoresis is used to visualize fluorescently stained DNA bands following separation. The stain binds to the DNA and under UV illumination, the DNA bands are visualized.
• Ethidium bromide, though extremely carcinogenic in small quantities, can be used however, SyberSafe is a safer alternative
• The DNA ladder contains DNA fragments of known sizes, through samples are compared to the ladder, in which the sizes of the DNA samples can be determined.

Agarose Gel Electrophoresis Steps

• Pour agarose and buffer solution into a plastic tray and place a comb on one end.
• Allow the agarose polymerizes into gel as it cools, then remove the comb to form wells for samples.
• Pipette DNA samples colored with a tracking dye are pipetted into the wells.
• Place the tray into a chamber that generates electric current through the gel, the negative electrode on the side nearest the samples, and the positive electrode on the other side.
• As DNA has a negative charge, and will be drawn to the positive electrode and smaller DNA molecules travel faster.
• Load one well with a DNA ladder, containing DNA fragments of known sizes, used to determine other samples sizes.

Conclusion

• DNA functions to allow for packing densely.
• There are two types of RNA.
• DNA contains hereditary material that results in gene expression.
• Gene mutations can occur during replication that may result in disease or illness.
• DNA can be separated based on size and charge via Gel Electrophoresis.

Explore Nucleic Acid Structure with a focus on DNA, as part of the Level 6 Certificate in Food Science and Technology. Understand DNA structure, nucleotides, the double helix, and more. Learn about gene mutations and DNA analysis methods.