Nucleic Acids, DNA, and RNA

• Nucleic acids are composed of a pentose sugar, a nitrogenous base, and a phosphate group.
• Genes contain the information that determines the characteristics of a species and its individuals.
• Rosalind Franklin discovered the structure of DNA using X-ray diffraction.
• The two major groups of nucleic acids are deoxyribonucleic acids (DNA) and ribonucleic acids (RNA).

Pentose Sugars

• DNA contains deoxyribose, while RNA contains ribose.
• The key difference is that RNA has a hydroxyl group on Carbon 2, which is absent in DNA.

Nitrogenous Bases

• There are five types of nitrogenous bases: adenine, guanine, thymine, cytosine, and uracil.
• Adenine and guanine are purines (2 rings).
• Thymine, cytosine, and uracil are pyrimidines (1 ring).

Differentiating Purines

• Adenine has an amino group on its 6-membered ring.
• Guanine has an amino group and a carbonyl group on its 6-membered ring.

Differentiating Pyrimidines

• Cytosine has an amino group and a carbonyl group on its 6-membered ring.
• Thymine has two carbonyl groups and a methyl group on its 6-membered ring.
• Uracil has two carbonyl groups on its 6-membered ring.

Nitrogenous Bases in DNA

• DNA typically contains adenine, guanine, thymine, and cytosine.

Nitrogenous Bases in RNA

• RNA usually contains adenine, guanine, uracil, and cytosine.

Nucleosides

• A nucleoside consists of a nitrogenous base covalently bonded to a pentose sugar via an N-glycosidic bond at the C1 position.

Nucleosides vs Nucleotides

• Nucleotides contain phosphate groups, whereas nucleosides do not.

Nucleoside Names

• Adenine nucleoside: Adenosine
• Guanine nucleoside: Guanosine
• Cytosine nucleoside: Cytidine
• Thymine nucleoside: Thymidine
• Uracil nucleoside: Uridine

Nucleoside Triphosphates (NTPs)

• Nucleoside triphosphates are nucleotides with three phosphate groups.
• NTPs are prime sources of chemical energy.
• ATP (adenosine triphosphate) is the energy currency of the cell.
• CTP (cytidine triphosphate) is essential in phospholipid biosynthesis.
• GTP (guanosine triphosphate) is the major energy source for protein synthesis.
• UTP (uridine triphosphate) is essential in carbohydrate biosynthesis.

AZT

• AZT (3'-azido-2'-3'-dideoxythymidine) is analogous to thymidine.
• AZT is an antiretroviral drug used to treat HIV/AIDS by inhibiting nucleoside reverse transcriptase.

Acyclovir

• Acyclovir is analogous to guanosine.
• Acyclovir is an antiviral drug that slows the growth and spread of the herpes virus.

Adenosine Functions

• Local hormone or autocoid
• Affects blood vessel dilation
• Involved in neurotransmitter release

Nucleotide Components

• A nucleotide comprises a pentose sugar, a purine or pyrimidine base, and a phosphate group.

Nucleotide Functions

• Building blocks of nucleic acids
• Sources of chemical energy
• Regulatory molecules

Nucleotide Names

• Adenine nucleotide: Adenylate
• Guanine nucleotide: Guanylate
• Cytosine nucleotide: Cytidylate
• Uracil nucleotide: Uridylate
• Thymine nucleotide: Thymidylate

Base Types

• Adenine and cytosine are amino bases.
• Guanine and thymine are keto bases.

Erwin Chargaff's First Rule

• The number of purines equals the number of pyrimidines.
• The percentage of A+T equals the percentage of G+C.

Erwin Chargaff's Second Rule

• The base ratio (A+T/G+C) varies widely between species but remains constant within a species.

Limitation of Chargaff's Rule

• It does not apply to single-stranded nucleic acids like ssDNA and ssRNA.

Base Pairing

• Adenine pairs with thymine, forming 2 hydrogen bonds.
• Guanine pairs with cytosine, forming 3 hydrogen bonds.

Nucleic Acid Backbone

• The sugar and phosphate groups form the backbone of nucleic acids.

Phosphodiester Bonds

• Phosphodiester bonds hold the backbone of polynucleotides together.

Phosphate Groups

• Each pentose sugar of the polynucleotide has a phosphate group on both the 3' carbon and the 5' carbon.

Hydroxyl Groups

• Hydroxyl groups (-OH) are present at the 3'C and 5'C for phosphate groups to react with.

DNA Secondary Structure

• Watson and Crick proposed the secondary structure of DNA.
• DNA is made of two complementary, antiparallel polymeric strands forming a right-handed double helix.
• Sugar and phosphate groups are linked by 3'-5' phosphodiester bonds.
• Purine and pyrimidine bases are flat and at right angles to the sugar-phosphate backbone.
• One full turn (pitch) measures 3.4 nm or 34 angstroms, and there are 10 base pairs per turn.
• Bases are separated by a spacing of 0.34 nm (3.4 angstroms).
• The width/diameter of the double helix is 2 nm (20 angstroms).

DNA Helix Bonds

• Weak hydrogen bonds hold the DNA helix structure together.

DNA Double Helix Features

• The sugar-phosphate backbone is on the outside of the helix, interacting with the polar environment.
• The nitrogenous bases are inside, stacking perpendicular to the helix axis.

DNA Conformations

• The three major forms of DNA conformations are A-form, B-form, and Z-form.

Factors Affecting DNA Conformation

• Hydration level of the molecule
• Sequencing of the nucleotides
• Degree of supercoil
• Chemical modifications (methylation or glycosylation)

B-Form DNA

• It is the most abundant form in cells.
• It is long, thin, and hydrated (72 H2O molecules per 12 bps).

A-Form DNA

• It is an unnatural form, existing during DNA extraction
• It is shorter, more compact, and dehydrated
• RNA molecules and DNA-RNA intermediates often have this form

Z-Form DNA

• It is a left-handed helix with a zig-zag sugar-phosphate backbone.
• Repeating units of dinucleotides instead of mononucleotides. (GCGCGCGCGCGCG).
• The pitch length is 4.5 nm (45 Å) with 12 bps per turn.
• Occurs in areas of active transcription and when DNA is methylated or halogenated.

Helix Handedness

• A-form and B-form DNA have right-handed helices.
• Z-form DNA has a left-handed helix.

Base Pairs per Turn

• A-form DNA has 11 bps per turn.
• B-form DNA has 10 bps per turn.
• Z-form DNA has 12 bps per turn.

Helix Width/Diameter

• A-form DNA has a width of 2.6 nm.
• B-form DNA has a width of 2.0 nm.
• Z-form DNA has a width of 1.8 nm.

Pitch Length

• A-form DNA has a pitch length of 2.8 nm.
• B-form DNA has a pitch length of 3.4 nm.
• Z-form DNA has a pitch length of 4.5 nm.

Bacterial DNA

• Bacterial DNA is circular.

Linear DNA

• Phages and some viruses have linear DNA.

DNA Supercoiling

• DNA naturally exists in cells as a negative supercoil (right-handed supercoil).

Relaxed DNA

• If DNA is not supercoiled, it is in a relaxed form.

Significance of Supercoiling

• Supercoiling allows DNA to fit into the confined space of the nucleus or nucleoid, making it compact.

Differences Between RNA and DNA

• DNA has a single function, while RNA has many functions.
• RNA has ribose sugar, while DNA has deoxyribose sugar in its backbone.
• RNA uses uracil, while DNA uses thymine.
• RNA is typically single-stranded, while DNA is typically double-stranded.

Types of RNA

• Three types of RNA involved in protein synthesis: mRNA, tRNA, and rRNA.

Messenger RNA (mRNA)

• A complementary copy of DNA, representing a copy of genes.
• Synthesized during transcription and is single-stranded
• mRNA is the least abundant cellular RNA (5%).

Transfer RNA (tRNA)

• Small molecules that carry specific amino acids during protein synthesis.
• Has a cloverleaf structure.
• Possesses anticodons that are complementary to the codons on mRNA
• There are 20 types of tRNA in cells.
• tRNA makes up 15% of cellular RNA.

Ribosomal RNA (rRNA)

• The most abundant type of RNA in cells.
• A component of ribosomes.
• Ribosomes are made of rRNA and proteins.

Prokaryotic rRNA

• Prokaryotes have three types of rRNA: 5S, 16S, and 23S.

Eukaryotic rRNA

• Eukaryotes have four types of rRNA: 5S, 5.8S, 18S, and 28S.

Prokaryotic Ribosomes

• Prokaryotes have 70S ribosomes with a large 50S subunit and a small 30S subunit.

Eukaryotic Ribosomes

• Eukaryotes have 80S ribosomes with a large 60S subunit and a small 40S subunit.

Other Types of RNA

• snRNA (small nuclear RNA) is involved in mRNA processing.
• snoRNA (small nucleolar RNA) is involved in rRNA processing.
• scRNA (small cytoplasmic RNA) is involved in the selection of proteins for export.
• miRNA (microRNA) is involved in RNA silencing and post-transcriptional regulation of gene expression.
• siRNA (small interfering RNA) interferes with the expression of specific genes.
• Ribozymes or catalytic RNA are involved in enzymatic or catalytic activities.

RNA Structures

• Secondary and tertiary structures of RNA include stem-loops, hairpins, and pseudoknots.

DNA Denaturation

• During DNA denaturation, hydrogen bonds are affected, while N-glycosidic and phosphodiester bonds are not.

DNA Renaturation

• Upon removal of the denaturant, DNA will reanneal, reforming the hydrogen bonds.

Denaturants

• Examples of denaturants include strong bases, concentrated salts, high temperatures, decreased dielectric constants by ketones and alcohols, and exposure to amides and urea.

Steps in Temperature-Based DNA Denaturation

• As temperature increases, bases unstack, and hydrogen bonds break, forming a bubble (A/T rich areas unwind first).
• At higher temperatures, even G/C rich regions are disrupted, leading to total denaturation.
• When the solution is slowly cooled, complementary regions form base pairs (nucleation).
• Renaturation is rapid due to zippering once nucleation occurs, reforming the double helix.

DNA Denaturation Definition

• DNA is denatured when it changes from a double helix to a random coil/ssDNA.

Melting Temperature (Tm)

• The melting or transition temperature (Tm) is the temperature at which half of the DNA strands separate or melt.

Lambda Max of DNA

• The lambda max of DNA is 260 nm.

Hyperchromic Effect

• The hyperchromic effect is the increase in absorption observed for ssDNA.