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Nucleotides, DNA, and RNA

Last updated: March 3, 2021

Summarytoggle arrow icon

The genetic information of an organism is stored in the form of nucleic acids. Nucleic acids, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are long linear polymers composed of nucleotide building blocks. Each nucleotide is comprised of a sugar, a phosphate residue, and a nitrogenous bases (a purine or pyrimidine). DNA is longer than RNA and contains the entire genetic information of an organism encoded in the sequences of the bases. In contrast, RNA only contains a portion of the information and can have completely different functions in the cell.

DNA is structurally characterized by its double helix: two opposite, complementary, nucleic acids strands that spiral around one another. The DNA backbone, with alternatively linked sugar and phosphate residues, is located on the outside. The bases are located inside the helix and form the base pairs adenine and thymine or guanine and cytosine, which are linked by hydrogen bonds.

The human genome comprises 3.2 x 109 base pairs, which are distributed over 23 pairs of chromosomes. Each chromosome is a linear DNA molecule of a certain length. The chromosome is only well visualized under the light microscope during the metaphase of mitosis, as it is maximally condensed during this phase. Chromosomes are present as pairs in most cells of the body. One chromosome in each of the 23 pairs originates from the mother and the other from the father.

Both interrelated chromosomes are termed homologous because they each have a variant of the same gene. Alterations in the number or structure of the chromosomes lead to various conditions, e.g., developmental disorders. Chromosomal assessment with different molecular biology and cytogenetic methods often allows for a clear diagnosis.

Nucleotides

NucleoSides consist of base and Sugar (deoxyribose). NucleoTides consist of base, deoxyribose and phosphaTe.

Nucleobases

Overview of pyrimidines and purines
Rings Base Notable characteristics As a nucleoside unit in RNA As a nucleoside unit in DNA
Pyrimidines
  • 1 ring
  • Cytosine (C)
  • Cytidine
  • Deoxycytidine
  • Thymine (T)
  • Not present
  • Thymidine
  • Uracil (U)
  • Uridine
  • Not present
Purines
  • 2 rings
  • Adenine (A)
  • Deoxyadenosine
  • Guanine (G)
  • Guanosine
  • Deoxyguanosine

A mean person GAGs a PURring cat!” (Three Amino acids, Glycine, Aspartate, and Glutamine, are necessary for PURine synthesis.)

C-G stabilizes DNA Crazy Good!” (C-G bonds are extremely stable.)

PYRates Capture 1 Undersea Treasure.” (PYRimidine bases: Cytosine, Thymine, and Uracil and consist of 1 ring.)
PURe A Glass for 2.” (PURine bases are Adenine and Guanine and consist of 2 rings.)

Thymine contains a methyl group and is only found in DNA; uracil is only found in RNA.

Nucleic acid sugars

  • Structure: The sugar found in nucleic acids is a pentose, which has a five-atom ring.
    • DNA is deoxyribose
    • RNA is ribose
  • Pentose binds
    • Bases via N-glycosidic bonds
    • Phosphate residue via phosphodiester bonds

Phosphate group

  • A nucleotide can have one, two, or three phosphate groups (also termed “nucleoside monophosphate”, “diphosphate”, and “triphosphate”, respectively).
  • Nucleic acids are composed of nucleoside monophosphates.
  • Nucleoside diphosphates and nucleoside triphosphates (e.g., ATP) are found in biochemical processes requiring energy
    • The phosphoanhydride bonds store a high amount of energy that can be utilized in biochemical processes when targeted by 3' hydroxyl attack.
    • The nucleotide that is added to the 5' end of the nucleic acid initially has three phosphate groups. The splitting of the two end phosphate groups supplies the energy necessary for the phosphodiester bonds that build the DNA backbone.

Nucleotide and nucleotide derivatives have important functions in the body.

The energy carrier ATP contains ribose and not deoxyribose as a sugar, and therefore has a 2' OH group!

Nucleic acids

Comparison of DNA and RNA

DNA vs. RNA
DNA RNA
Bases
Sugar
  • Deoxyribose
  • Ribose
Length
  • Depending on the organism
  • Ranging from several thousand to several millions of nucleotides
  • Varies considerably
Structure
  • Usually single-stranded (except the double-stranded miRNA and siRNA)
  • Various 3D structures are possible; e.g., loops through the formation of short sections with base pairing (double-stranded)
Function
  • Carries the hereditary information (collectively known as the genome) for the construction and function of the organism
  • Varies considerably depending on class, e.g., coding, regulatory, or enzymatic function (see table “Classification of RNA” below)

Overview of double-stranded DNA

Organization of the human genome

Double helix

  • 3D structure of DNA in which two polynucleotide strands are intertwined, stabilized by:
    • Specific base pairing via hydrogen bonds (H bonds) between complementary nucleobases of DNA
      • A-T bonds consist of 2 H bonds
      • G-C bonds consist of 3 H bonds, resulting in a stronger bond (an ↑ in G and C in DNA ↑ melting temperature of DNA)
    • Hydrophobic effect: The negatively charged sugar-phosphate backbone is located on the outside of the helix, the bases on the inside.
    • Base stacking: The base pairs are stacked on one another (stacking interactions) and interact through van der Waals forces, which have an additional stabilizing effect.
  • Double helix has a minor groove and a major groove.

Conformations

  • B conformation (B-DNA)
    • Most prevalent
    • Right-handed double helix
    • 10 base pairs per helical twist to a length of 3.4 nm
    • Diameter of the helix: 2 nm
    • Bases are approx. perpendicular to the helix axis.
  • A conformation (A-DNA)
    • Right-handed double helix, although broader and shorter than B-DNA
    • Base pairs are not perpendicular to the helix axis but are slightly inclined toward the axis.
    • Dehydrated form, i.e., present under experimental conditions and not in vivo.
  • Z conformation (Z-DNA)
    • Left-handed double helix
    • Stretched longer than B-DNA resulting in a smaller diameter
    • Occurs in GC-rich sequences, although they are generally rare under physiological conditions
    • The phosphate groups of the DNA backbone form a zigzag pattern.

Base pairs in DNA: guanine pairs with cytosine (3 H bonds), adenine pairs with thymine (2 H bonds).

Supercoils

Palindrome

  • Description
    • A palindrome is a sequence that reads the same forwards and backward (e.g., eye, level, madam).
    • The molecular biological use of the term “palindrome” is for inverted repeats (repeated sequence in the opposite direction).
  • Occurence
    • In palindromic sequences, a sequence of base pairs occurring over a certain segment is read identically on both complementary DNA strands, i.e., the sequence always reads the same on both strands in a 5'→3' direction.
    • Bases may be present between the palindromic sequences that are not complementary.
    • These segments are self-complementary and can form a hairpin loop.
    • Results in the formation of a cross-shaped structure in double-stranded DNA
  • Function: Some proteins that are capable of binding DNA require palindromic sequences as a recognition sequence, e.g., steroid hormone receptors or restriction enzymes.

Chromatin

Heterochromatin is Hooked tight while Euchromatin is Easygoing.

Histones

Histone Methylation Mutes transcription. Histone Acetylation Activates transcription.

Nucleosome (nucleosome core particle)

  • Definition: a structural and functional complex of DNA (∼ 150 bp) and histone octamer that gives chromatin its “beads on a string” appearance
  • Structure
    • DNA wraps around the nucleosome core with ∼ 1.8 twists
    • Nucleosomes are linked to one another through linker DNA (short DNA segment of variable lengths)
  • 30 nm chromatin fiber (solenoid)
    • Nucleosome strand that is spirally bound to fibers with a diameter of 30 nm
    • Each twist of the 30 nm fiber contains ∼ 6 nucleosomes.
  • Chromatin loop
    • Condensed form of DNA beyond the nucleosome and 30 nm fibers
    • The histone H1 and nonhistones are involved in the formation of loops.

Chromosomes

See “Basics of human genetics” for more information.

Human genome

Nuclear genome

Mitochondrial genome (mitochondrial DNA, mtDNA)

RNA classes and their structure

RNAs can be differentiated into various types, which differ in their length, structure, and function. Depending on the type, RNA can be a single-stranded or double-stranded segment.

Classification of RNA
Function Structure
mRNA (messenger RNA)
  • Very variable structure and length, because the nucleotide sequence of mRNA depends on the nucleotide sequence of the corresponding DNA segment
  • In eukaryotes, the initial transcript from DNA is known as heterogeneous nuclear RNA (hnRNA).
  • pre-mRNA: hnRNA that undergoes posttranscriptional modifications to become mRNA
tRNA (transfer RNA)
rRNA (ribosomal RNA)
snRNA (small nuclear RNA)
snoRNA (small nucleolar RNA)
RNA component of signal recognition particles
(scRNA; small cytoplasmic RNA)
  • 7S RNA, in addition to the six protein components of the signal recognition particles (SRP), which is responsible for the transport of newly formed proteins in the ribosome to intracellular compartments in the cytoplasm
  • Composed of 300 nucleotides
  • Complex structure with many double-helical segments
Telomerase RNA component (human telomerase RNA, hTR)
miRNA (microRNA)
  • Class of regulatory, noncoding RNAs, naturally found in cells in the form of hairpin structures
  • Encoded in introns
  • Regulates gene expression
    • Binding of the 3' untranslated region via nucleotide pairing prevents translation and accelerates the degradation of certain mRNA.
    • miRNA binds loosely to mRNA, thereby allowing a higher number of related mRNAs to bind it.
    • Dysfunctional miRNA expression may contribute to the development of some cancers (e.g., a miRNA that silences the mRNA of a tumor suppressor gene).
  • Composed of ∼ 20–30 nucleotides
  • Formed from precursor molecules with a 5' cap and a poly(A) tail, but are then cleaved into smaller oligonucleotides
siRNA (small interfering RNA)
  • Class of regulatory, noncoding RNAs that most commonly arise from exogenous dsRNA sources (e.g., viruses)
  • Regulates gene expression via highly specific nucleotide pairing → mRNA degradation → mRNA translation
  • Experimental use: gene “knockdown”
  • Composed of ∼ 20–30 nucleotides
  • Formed from double-stranded precursor molecules from a similar mechanism as for miRNA

To remember the features of the two tRNA arms, think: “Dihydrouridine and Detection” for the D-arm and “tRNA Tethering” for the T-arm.

CCA Can Catch Amino acids” (function of the 5'-CCA-3' sequence in tRNA).