Nucleic Acids: DNA and RNA

• Nucleic acids got their name since they were first discovered in the nucleus of cells.
• Nucleic acids exists in two structural forms: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
• Nucleotides serve as the building blocks of nucleic acids, and both DNA and RNA are polymers of nucleotides.

Nucleotide Structure

• A nucleotide consists of a nitrogenous base, a pentose sugar (5-carbon sugar), and a phosphoric acid group (phosphate group).
• Nucleotides are a combination of a nitrogenous base, a sugar, and a phosphate group, all connected to form a nucleic acid chain (polynucleotide).
• A nucleoside is a combination of sugar and base.
• Nucleotides have five different bases and two different sugars.
• Nitrogenous bases of nucleic acids include purines and pyrimidines.
• Purines (adenine (A) and guanine (G)) are composed of two fused rings incorporating two nitrogen atoms each.
• Pyrimidines (cytosine (C), thymine (T) and uracil (U)) are composed of a single ring with two nitrogen atoms.
• Adenine (A), guanine (G), and cytosine (C) are found in both DNA and RNA.
• Thymine (T) is only found in DNA, and uracil (U) is only found in RNA.
• In the formation of a nucleic acid, a hydrogen atom is lost during the combination of other elements.

Purines and Pyrimidines

• Thymine (T) is a pyrimidine found in DNA.
• Uracil (U) is a pyrimidine found in RNA.
• Cytosine (C) is a pyrimidine found in both DNA and RNA.
• Guanine (G) and Adenine (A) are purines that are present in both DNA and RNA.

Pentose Sugar

• D-ribose and D-deoxyribose are the 5-carbon sugars found in nucleic acids.
• DNA and RNA have different sugar moieties.
• RNA nucleotides contain ribose sugars (ribonucleotides).
• DNA nucleotides contain deoxyribose sugars (deoxyribonucleotides).

Phosphoric Acid

• Phosphoric acid, when in ionized form, is referred to as phosphate.
• Nucleotides are linked together via their phosphoric acid portions.
• The components of a mononucleotide are joined by two condensation reactions, with one occurring between the sugar and the phosphate and the other between the sugar and the nitrogenous base.

From Nucleoside to Nucleotide to Nucleic Acid

• Nucleic acids form when a nitrogen base and a 5-carbon sugar combine to form a nucleoside.
• A nucleoside joins with phosphoric acid to form a nucleotide.
• Combining nucleotides become nucleic acid.
• Nitrogen base + 5-carbon sugar = nucleoside.
• Phosphoric acid + nucleoside = nucleotide.
• Nucleotide becomes nucleic acid.
• A compound with hydrogen (nitrogen base) approaches another molecule containing an -OH group (sugar), resulting in the hydrogen combining with the -OH to form water (expelled). Subsequently a bond forms in the remaining fragments.

Nucleotide Naming Rules

• For ribose sugars, base name usage results in adenine becoming adenosine
• For deoxyribose sugars, adding a "deoxy-" prefix results in adenine becoming deoxyadenosine

Reactions, Esters and Nucleotides

• Phosphate ester of a nucleoside forms through a condensation reaction between the phosphoric acid and the alcohol group (OH-) on carbon number 5, -CH2OH.
• Adenosine monophosphate (AMP) is an example of a nucleotide.
• Nucleotides are the monomers from which nucleic acids form.
• AMP is one of the building blocks of RNA and is involved in energy transfer in cells.
• If a sugar is ribose, the result is one of four ribonucleotides. If a sugar is deoxyribose, result is one of four deoxyribonucleotides.

Nucleic Acids

• Nucleic acids are formed when nucleotides join using a condensation reaction.
• A condensation reaction involves the phosphate group of one nucleotide reacting with the alcohol group on carbon atom number 3' of another nucleotide.
• In the structure of a nucleotide, the lower -OH group is phosphoric acid attached to carbon-5', while the upper -H is alcohol on carbon-3'.
• The start of a polymer end is 5’, while the terminal end is 3’.

DNA and RNA Similarities

• Both are large molecules located in cell nucleus.
• DNA and RNA store and direct information for cell reproduction/growth.

DNA and RNA differences:

• DNA stores genetic information in its structure.
• DNA uses the template strand involved in replication and transcription.
• RNA transfers genetic information from DNA.
• RNA delivers instructions to ribosomes for protein synthesis.

DNA and RNA Together

• They enable life and are known as the central dogma of genetics.
• Both are nucleotide polymers. DNA is larger.
• DNA has 3 billion nucleotides in humans.
• DNA is Written as: 5'-C-G-T-A-3' (example sequence).
• DNA has 1-100 million nucleotides and viral DNA is smaller.

RNA Types and Sizes:

• rRNA (75-80%) has 120 - 3,700 nucleotides.
• tRNA (10-15%) has 70-90 nucleotides.
• mRNA (remainder) has approximately 1,200 nucleotides.

Role of each RNA

• Ribosomal RNA (rRNA) is located in ribosomes and its the site of protein synthesis.
• Transfer RNA (tRNA) transfers amino acids to ribosomes.
• Messenger RNA (mRNA) carries DNA's instructions to ribosomes and guides protein assembly sequence.

Additional Functions of RNA:

• RNA components are present in ATP, cAMP, FAD, and NAD+.
• RNA is found in all plants and animals.
• Viruses may contain either DNA or RNA.

DNA Functions

• In most organisms, DNA serves as the genetic material.

RNA roles include RNA as a genetic material:

• In some viruses such as the influenza virus, RNA acts as the genetic material.
• Messenger RNA (mRNA) serves as the carrier of genetic information to the site of protein synthesis.
• Transfer RNA (tRNA) links messenger RNA and amino acids, coupling them in protein synthesis.
• Ribosomal RNA (rRNA) is an essential component of ribosomes.

DNA Structure

• DNA is made of 2 polynucleotide strands held together by hydrogen bonds.
• Strands of DNA are lined up with the bases pointing towards each other.
• The strands run in opposite directions, i.e., they are anti-parallel.
• One strand runs from 5' to 3', while the other runs from 3' to 5'.
• A, T, C, G base pairing rules:
  • A pairs with T (with 2 hydrogen bonds).
  • G pairs with C (with 3 hydrogen bonds).
  • In RNA, A pairs with U
• Strands mirror each other, therefore each of these pairs is one purine bonded to one pyrimidine, and are said to be complementary.
• Knowledge of the sequence of one strand allows predicting the sequence of the other strand.
• DNA strands twist together into a double helix.
• B-Form DNA, a double helix is the most common DNA Structure.

DNA double helix shape:

• DNA is a double helix (like a twisted ladder).
• It is a right-handed spiral (turns clockwise looking down).
• DNA is present in most common form in living cells.

Measurements of the double helix:

• Width = 2 nanometers.
• Space between each base pair = 0.34 nm.
• One full turn contains 10 base pairs and equals 3.4 nm long.
• Hydrogen bonds and base stacking force (hydrophobic interaction) are responsible for its stable configuration.

Prokaryotic DNA Organization

• The organization differs between prokaryotes and eukaryotes.
• In cells, DNA is packaged efficiently to fit in the cell and be functional.
• DNA exists as a supercoil, which is a compact twisted structure.
• Supercoiling is essential for packaging DNA within the small cell space.
• DNA is free in the cytoplasm (no nuclear membrane).

Eukaryotic DNA Organization

• DNA is highly organized and packaged within the nucleus in these cell types.
• The structure alternates between two main forms: Chromatin and Chromosomes.
• Chromatin is a looser, accessible form during most of the cell cycle.
• Chromosomes exist as a highly condensed form that appears during metaphase.
• The fundamental packaging unit is the nucleosome, consisting of DNA wrapped around histone proteins.
• Chromosomes are a compact form of the DNA that readily fits inside the cell.
• They protect DNA from damage.
• DNA in a chromosome is transmitted efficiently to both daughter cells.

Chromosomes

• Each chromosome confers an overall organization to each molecule of DNA.
• They facilitates gene expression and recombination.

Genes

• A gene is the minimum functional unit in DNA.
• The genome represents all genes in a living cell or being.
• Sequence of nucleotides along a DNA molecule that codes for polypeptide (protein) product.
• Every triplet of nucleotides codes for one amino acid.
• A sequence of 3 bases (a triplet) is called a codon.
• Genetic code determines which triplet of nucleotides codes for which amino acid.
• DNA nucleotides have the same structure (concerning sugar and phosphate group), and differ only in nitrogenous bases.
• The sequence of bases in DNA determines the sequence of amino acids in a polypeptide chain.
• There are only 4 bases in DNA: G, C, A, T, but 20 amino acids are found in polypeptides.
• If every three bases coded for one amino acid, there would be a maximum of 64 (43) different amino acids.
• The standard code (in "DNA language") has a scheme that is read from the inside to the outside.
• Nature uses a triplet code comprised of three bases per amino acid.
• The extra combinations (64 versus 20 needed) allow for multiple codons coding for the same amino acid (redundancy).
• The standard code has special "stop" and "start" signals in the genetic code.
• The genetic code is degenerate because many amino acids are coded by more than one triplet codon.
• Some triplets' codons are called stop codons.
• Protein synthesis stops when it reaches one of these codons.
• The genetic code is specific with a specific codon always coding the same amino acid.
• The genetic code is universal, meaning the same codons are used in living organisms (prokaryotes + eukaryotes).
• A degenerate or redundant genetic code allows each codon to correspond to a single amino acid, and one amino acid may have more than one codons (e.g., arginine has 6).
• A human genome is the total amount of genetic material, divided into 46 molecules of DNA (each called a chromosome).
• Linear DNA from a single cell is 2 meters in length, and human cells contain roughly that amount.

Protein Synthesis:

• DNA never leaves the nucleus due to its large size and inability to fit through nuclear pores.
• Protein synthesis takes place on ribosomes located in the cell cytoplasm.
• The genetic information stored in the DNA is carried by messenger RNA (mRNA) from the nucleus to the ribosome.
• Messenger RNA (mRNA) acts as a messenger between DNA and proteins.
• mRNA is created using DNA as a template (C-G, A-U).
• The molecule is a single-stranded and has a temporary existence which is degraded after protein synthesis.
• mRNA can exit the nucleus through nuclear pores to travel to the cytoplasm.

RNA Structure

• RNA does not contain Thymine (T); instead, it contains Uracil (U).
• DNA Base pairing in RNA is as follows
  • Guanine (G) >> Cytosine (C).
  • Cytosine (C) >> Guanine (G).
  • Adenine (A) >> Uracil (U).

Transfer RNA (tRNA)

• Each tRNA molecule is specific for a particular amino acid.
• There are 20 different tRNAs, one for each amino acid.
• At one end of the molecule, the appropriate amino acid binds.
• At the other end, it bears a three base sequence complementary to the triplet codon on mRNA.
• This region is called the anti-codon.
• tRNA binds to its amino acid in the cytoplasm and transfers it to the site of protein synthesis (the ribosome).
• tRNA has a complex secondary structure due to many intra-strand hydrogen bonds.
• There are 45 different tRNA molecules as an smaller number of tRNA is needed due to the wobble base effect.
• Wobble bases means that for some codons, the complementary anti-codon can show some flexibility in the third base.
• This means that the third base is not following the regular rules for pairing.
• The exceptions to the codon rules for wobble pairing are:
  • If a codon ends in G: It's anticodon can use either C or U - This breaks the usual G-C pairing rule.
  • If a codon ends in U: It's anticodon can use either A or G - This breaks the usual U-A pairing rule.
• Two bases remain strict in their pairing:
  • A at the end of a codon only pairs with U
  • C at the end of a codon only pairs with G
• Ex: The wobble pairing allows one type of tRNA to match more than one mRNA as Histidine can be coded by either CAC or CAU.
• Histidine and GUG can recognize both codons, however the first two bases must match exactly, and the third position (G) can pair with either C or U.
• The triplet base sequence at the anticodon is directly related to the amino acid carried by that tRNA molecule.

Ribosomal RNA (rRNA)

• The third form of RNA is rRNA.
• It is associated with some protein molecules.
• rRNA forms the ribosomes, which are protein synethesis sites.

Protein Synthesis

• Requires two processes called Transcription and Translation.
• Transcription converts DNA to RNA and occurs in nucleus
  • Transcription uses RNA polymerase
  • Transcription makes a mRNA copy of gene
  • Transcription uses template DNA to turn out complementary RNA

Translation

• The movement of ribosome along mRNA and occurs during protein synthesis.
• Move exactly 3 nucleotides (1 codon).
• Powered by ATP energy.
• Transcription (occurs in the nucleus) is the synthesis of a molecule of RNA using the enzyme RNA polymerase that is complementary to the gene sequence on DNA.
• RNA polymerase attaches to the double stranded DNA at the start codon which is the codon for methionine.
• It breaks the hydrogen bonds holding the strands, causing the DNA to unwind into template and coding strands which loses its helical shape).
• In transcription: RNA polymerase catalyzes the synthesis of mRNA using one of the DNA strands (Template strand).
• This template strand of gene is transcribed into RNA giving template and generated mRNA complementary sequences.
• The other DNA strand is the coding strand and shares an identical sequence with the formed RNA except that transcription excises and removes introns, and then joins togetther the remaining exons with the mature mRNA in a process called splicing.
• Protein expression requires a translated "nucleic acid language" to be translated into "protein language"
• This is the origin of the term translation to describe protein biosynthesis, utilizing the genetic code as the dictionary.

Translation Steps

• The mRNA travels through the nuclear pore and binds to a ribosome exposing two codons
• The tRNAs specific for these codons form hydrogen bonds with mRNA and the tRNAs
• Attached amino acids are joined together starting protein formation.
• After a peptide bond is formed, the ribosome physically moves along the mRNA one codon in length exposing another codon ready for its tRNA.
• This happens until the amino acids are bonded together at which point they separate from tRNA
• The tRNA leaves the ribosome and becomes ready to pick up another amino acid.
• Translation ceases upon reaching a stop codon and a release factor is bound and results in no tRNA molecule for that codon.
• In this case the ribosome "falls off" the mRNA ending synthesis.