Molecular Biology: Nucleic Acids & DNA

• Foundation of Molecular Biology is Unit 2

Introduction to Nucleic Acids

• Nucleic acids are organic compounds found in all organisms, existing as DNA or RNA
• Nucleic acids form from nitrogenous bases, sugar molecules, and phosphate groups linked in a series of sequences
• DNA structure defines the basic genetic makeup of organisms

What is DNA?

• DNA is a group of molecules responsible for carrying and transmitting hereditary materials, referred to as genetic instructions, from parents to offspring

Role of DNA

• DNA, or Deoxyribonucleic Acid, is an organic compound possessing a unique molecular structure
• It is present in both prokaryotic and eukaryotic cells
• Nuclear DNA, located in the nucleus of eukaryotic cells, codes for most of an organism's genomes and is responsible for the inheritance of genetic information
• DNA plays a crucial role in protein production, demonstrated by the central dogma
• Mitochondrial DNA resides in the cell's mitochondria, inherited from the mother, and contains about 16,000 base pairs in humans
• Plastids in plants have their DNA and play an role in photosynthesis

Classes of Nucleic Acids

• DNA has one type and purpose
• RNA has several types and purposes
• Ribosomal RNA is the basis of structure and function of ribosomes
• Messenger RNA carries the message
• Transfer RNA carries amino acids
• MicroRNA regulates gene expression

RNA vs DNA

• RNA is Ribonucleic acid
• DNA is Deoxyribonucleic acid

Who Discovered DNA?

• Johannes Friedrich Miescher, a Swiss biologist, first recognized and identified DNA in 1869 during research on white blood cells
• The double helix structure of DNA was later discovered by James Watson and Francis Crick, based on experimental data
• DNA is responsible for storing genetic information in living organisms
• DNA comprises a sugar-phosphate backbone and nucleotide bases (guanine, cytosine, adenine, and thymine)

Physical and Chemical Properties of DNA

• DNA is polar and soluble in water, attributed to its charged phosphate-sugar backbone. It becomes insoluble when salt and alcohol are present
• At 260 nanometers, DNA bases can absorb ultraviolet light, measured by a spectrophotometer, increasing with base order
• At 260 nm, single-stranded DNA absorbs 1.37 units, whereas double-stranded DNA absorbs 1.00 unit

Denaturation and Renaturation

• On heating, both strands denature and can renature upon cooling
• Melting temperature, which varies by DNA sequence, is the temperature to which the strands are permanently separable
• Regions of higher C-G concentration have a higher melting temperature due to the presence of three hydrogen bonds, unlike A-T which have two hydrogen bonds

Watson and Crick Model of DNA

• Nucleoside is a compound formed by a pentose sugar and nitrogen base
• Nucleotide is a compound formed by a nucleoside and a phosphate group
• Nucleotides are the building blocks of nucleic acids
• Nucleotides have three components:
• A nitrogenous base
• A pentose sugar
• A phosphate group

The DNA Double Helix

• DNA double helix is stabilized by hydrogen bonds
• "Base pairs" are bound together with hydrogen bonds
• Erwin Chargaff had the base pairing data, but did not understand the implications
• Rosalind Franklin's X-ray fiber diffraction data was crucial
• Francis Crick knew it was a helix
• James Watson figured out the H-bonds

History of DNA Research

• In 1925, Linus Pauling used X-ray crystallography to determine the secondary structure of proteins
• X-ray crystallography was used for analyzing molecular structure and the patterns revealed details about the structure of molecules of interest
• In 1953, Rosalind Franklin used X-ray crystallography to explore the structure of DNA
• Watson and Crick worked together to put together the jigsaw of the DNA molecule using Franklin's discoveries
• Watson and Crick presented a model for the DNA's double-helix structure
• A nucleotide polymer makes up the DNA molecule

X-Ray Diffraction

• X-ray crystallography was first used to analyze the structures of organic minerals but expanded to complex molecules
• It aided in determining the alpha helix, beta sheets, hemoglobin, and DNA structures

DNA Structure Analysis

• In the early 1950s, studies showed that DNA produces a characteristic X-ray diffraction pattern
• DNA molecules are helical with two periodicities (3.4A and 34A) along their axis
• Important to formulate a three-dimensional model that accounted for X-ray diffraction data, Chargaff's base equivalence discoveries (A=T and G=C), and other chemical properties of DNA

Key Structural Dimensions by X-Ray Diffraction

• Distance between bases: 3.4A
• Length of period: 34A
• Rise of the helix: 36 degrees

Nobel Prize

• Watson and Crick were awarded the 1962 Nobel Prize in Physiology and Medicine for discovering the double helical structure of DNA
• Wilkins and Franklin contributed greatly to this discovery

Watson and Crick DNA Model

• In 1953, Watson & Crick proposed a three-dimensional model of DNA structure
• DNA consists of two helical chains wound around the same axis but are a right-handed double helix chain
• Alternating deoxyribose and phosphate groups form hydrophilic backbones on the helix exterior
• Purine and pyrimidine bases are stacked inside the double helix
• A hydrophobic planar ring structure is positioned very close together and perpendicular to the long axis

DNA Dimensions

• DNA diameter: 20 nm
• Length of DNA in E. coli: 1.6 million nm
• Diameter of the helix is uniform as a purine is paired with a pyrimidine
• The adjoining bases are 0.34 nm, or 3.4Å, along the axis apart
• A full helix turn: 3.4 nm or 34Å. 10b/turning

Postulates of DNA Structure

• Major and minor grooves of the DNA double helix are caused by the geometry of the bases
• Wider gap (major groove)
• Narrower gap (minor groove)
• Minor grooves (1.2 nm)
• Major grooves (2.2. nm)
• Grooves are important binding sites for proteins that maintain DNA and regulate gene activity
• Eukaryotic DNA is compacted with histones

Antiparallel and Reverse Polarity

• DNA strands are antiparallel: one strand is 3' to 5', while the other is 5' to 3'
• A 5' end (phosphate-bearing) of one strand aligns with the 3' end (hydroxyl-bearing) of its partner
• Two chains exhibit reverse polarity, running in opposing directions

Complementarity

• Each pair of bases lies flat, forming a "rung" in the DNA molecule's ladder
• Base pairing occurs between a purine and a pyrimidine
• Adenine (A) always pairs with thymine (T) through two hydrogen interactions
• Guanine (G) always pairs with cytosine (C) via three hydrogen bonds: A = T and G = C

Chargaff's Rules

• Σ purines (A+G) = ∑ pyrimidines (C + T)
• Also, (A + C) = (G + T).
• Ratio of (A + T) and (G + C) can be constants for a species from a range of 0.4 to 1.9

Factors Stabilizing DNA Double Helix

• Hydrophobic interactions bury hydrophobic purine and pyrimidine rings in the interior
• Stacking interactions involve van der Waals forces between stacked bases
• Hydrogen bonding occurs between bases
• Charge-Charge Interactions - Electrostatic repulsions of phosphate groups are minimized by cations like Mg

Base Sequence

• The base sequence of DNA varies throughout a polynucleotide chain, carrying the genetic information
• DNA molecules carry genes that store genetic information

DNA Types

• Three different DNA types: A-DNA, B-DNA, and Z-DNA
• A-DNA is a right-handed double helix similar to B-DNA, formed by dehydrated DNA to withstand desiccation or when protein binding removes solvents
• B-DNA: Majority of DNA demonstrates a B type conformation under physiological conditions
• Z-DNA winds to the left in a zig-zag pattern, discovered by Andres Wang and Alexander Rich. Found ahead of the start site of a gene

DNA Properties

• DNA is double-stranded
• Strands are antiparallel because they run in opposite directions
• Sugar-phosphate backbones, the orientation of the sugar molecule, is opposite in the two strands
• DNA is a polymer of nucleotides
• Sugar forms the structural framework of nucleic acids (DNA and RNA)
• Serves as the backbone, composing alternating sugar and phosphate groups, and defines directionality of the molecule
• DNA is called the blueprint of life since instructions are needed for an organism to grow, develop, survive, and reproduce
• DNA manages this by controlling protein synthesis because proteins structure and function in the cells of organisms