Nucleotides, DNA, and RNA

Abstract

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

Nucleotides

  • Structure
    • Nitrogenous base (a purine or pyrimidine)
    • A pentose sugar
    • Phosphate group
  • Bonds
    • Base + sugar → (N-glycosidic bond) → nucleoside + phosphate group at the 3' or 5' C atom of sugar → (ester bond) → nucleotide

Nucleobases

  • See learning card on purines and pyrimidines for more details.
Type of base 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)
  • Created from 5-methylcytosine via deamination
  • Also arises from methylation of uracil
  • Has a methyl group
  • Forms 2 H bonds
Not present Thymidine
Uracil (U) Uridine

Not present

Purines
  • 2 rings

Adenine (A)

Adenosine Deoxyadenosine
Guanine (G) (has a ketone)
  • Has a ketone group
  • Forms 3 H bonds
Guanosine Deoxyguanosine

CUT the PYrimidine;PURine As Gold.

Thymine is found in DNA; uracil is found in RNA.

A MEAN person GAGs a PURring cat!

Nucleic acid sugars

  • Structure: The sugar found in nucleic acids is a pentose, which has a five-atom ring. Specifically, the sugar in:
    • DNA = deoxyribose
    • RNA = 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 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.

Function of nucleotides and their derivates

Nucleotide and nucleotide derivatives have important functions in the body.

  • Building blocks of nucleic acids
  • Source of energy: especially as a universal energy carrier of the cell in the form of ATP, but also GTP
  • Signal molecules: especially the second messenger cAMP (cyclic adenosine monophosphate) and cGMP (cyclic guanosine monophosphate) , both phosphoric esters
  • Activators for the transfer of groups: Through the potential of forming energy-rich bonds, nucleotides are able to transfer a molecule onto another in biosynthesis, e.g.:
    • UDP-Glucose is an active form of glucose in gluconeogenesis.
    • Dietary choline can be activated to citicoline by CTP and be used in the synthesis of phosphatidylcholine.
    • 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) serves as a sulfate group donor in sulfatide synthesis.
    • S-Adenosyl methionine (SAM) is formed from methionine and serves as a cofactor in methylation reactions.
  • Regulators: enzyme reactions in signal transduction pathways (e.g., activates GTP G proteins)
  • Carrier molecules: e.g., the electron carrier nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD) as a component of coenzymes in redox reactions

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

Overview of nucleic acids

Nucleic acids

  • Long, linear chains (polymers) of nucleotides
  • Alternating sugar and phosphate residues of individual nucleotides, linked by phosphodiester bonds, form the backbone
  • Primary structure of nucleic acids: nucleotide sequence in the chain
  • Phosphodiester bonds are negatively charged.
    • Negative charges stabilize the nucleic acids.
    • Phosphodiester bonds cannot be easily hydrolyzed like other esters.
  • The chemical composition of nucleic acids (DNA and RNA) and their structure of repetitive nucleotide units allow them to function as both information carrier and mediator.

Comparison of DNA and RNA

DNA RNA
Bases
Sugar
  • Deoxyribose
  • Ribose
Length
  • Depending on the organism
  • Ranging from several thousand to several millions of nucleotides
  • Varies considerably
Structure
  • Depends on the RNA type but is usually single-stranded
  • 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)

DNA structure and the human genome

Overview of DNA structure and packaging

  • Organization of the human genome: Nucleotides form single-stranded DNA → stabilizes into double-stranded DNA → conforms into right-handed double helixchromatin formation begins when the double helix binds histone to form nulceosomes (appear as “beads on a string” under electron microscopy) → chromatin is further compacted → during replication (mitosis or meiosis), chromatin maximally condenses into chromosomes (only visible during metaphase under light microscopy)
  • DNA is very flexible in the longitudinal direction. DNA conformation can be affected by protein binding. The sequence of bases also has an effect on the local structure.

Double-stranded DNA

  • DNA is primarily a double-stranded chain of deoxyribonucleotides in cells
  • Both strands are complementary to each other and run anti-parallel .
  • Double helix: 3D structure of DNA in which two polynucleotide strands are intertwined
    • Stabilized by:
      • Specific base pairing via hydrogen bonds (H bonds) between complimentary nucleobases of DNA
        • A-T bonds consist of 2 H bonds
        • G-C bonds consist of 3 H bonds → stronger bond
          • Thus, 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.
    • The double helix of DNA has a minor groove and a major groove.
    • There are 3 DNA conformations (A-DNA, B-DNA, Z-DNA): The DNA present in cells is usually B-DNA and is, therefore, a right-handed double helix.
      • 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. Some RNAs and DNA-RNA hybrids adopt this conformation.
      • 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)!

Further structural characteristics of DNA

Supercoils

  • Definition: winded double helix , also termed “superhelix”
  • Occurrence: especially in circular DNA molecules
    • In prokaryotes: chromosome of bacteria, plasmids
    • In eukaryotes
  • Characteristics: Supercoiled DNA molecules have a more compact structure than the relaxed form of DNA.

Palindrome

  • Definition: A palindrome is a sequence that reads the same forwards and backward, e.g., Otto
  • The molecular biological use of the term “palindrome” is for inverted repeats (repeated sequence in the opposite direction).
  • In DNA, a palindrome is a sequence of base pairs that reads the same on two strands when the orientation of reading is kept the same. For example, the following sequences read the same on the two strands in 5'→3' direction.
    • 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

  • Definition: complex of DNA and its associated proteins (both histones and non-histones) structured as repetitive units (nucleosomes)
  • Function: condensation and organization of DNA structure (also influences gene regulation)
  • Types
    • Heterochromatin
      • Contains inactive DNA because the highly condensed, steric conformation does not allow transcription
      • Darker on electron microscopy (EM)
      • DNA methylation is ↑ and acetylation is ↓
      • Subtypes
    • Euchromatin
      • Contains active DNA because the less condensed steric conformation makes DNA accessible for transcription
      • Lighter on EM

Components of chromatin

Histones
  • Definition: group of proteins that bind to DNA in the nucleus of eukaryotes to support the structure of chromatin
  • Characteristics
    • Positively charged through the high percentage (∼ 25%) of basic amino acids (arginine and lysine)
    • Strong ionic interactions with negatively charged DNA
    • Synthesized in the cytosol and transported to the nucleus
  • Types: There are four core histones and a linker.

Histone Methylation Mainly 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
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 the “Basics of human genetics” for more information.

  • Description
    • A denser packaging of chromatin that only becomes visible under microscope during cell division (especially in metaphase)
    • Number of chromosomes in the human genome:
      • Somatic cells contain 23 pairs of homologous duplicated chromosome pairs (46 chromosomes in total).
      • Germ cells only contain 23 single-stranded, unduplicated chromosomes.
  • Structure: A chromosome pair consists of 2 identical chromatids connected at the center by a centromere.

Human genome

  • The human genome consists of ∼ 3.2 billion base pairs (bp).
  • The DNA stored in a human cell would total ∼ 1.8 m in length.
  • In addition to the nuclear genome (found in the nucleus), there is also a mitochondrial genome that largely codes for RNA-associated proteins

Nuclear genome

Mitochondrial genome (mitochondrial DNA, mtDNA)

RNA: Structure and characteristics

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)
  • Coding RNA that functions as a template for translation in protein synthesis
  • DNA is used as a template for mRNA synthesis in the nucleus by RNA polymerase (transcription)
  • See also gene expression and transcription
  • 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). hnRNA destined to become mRNA is also known as pre-mRNA, which undergoes the following processes in the nucleus to create mRNA:
    • 7-Methylguanosine cap structure at the 5' end
    • A polyadenylation tail at the 3' end
    • Spliced out introns
tRNA (transfer RNA)
rRNA (ribosomal RNA)
  • Fulfills structural and functional tasks (catalyst) as part of the ribosome during protein synthesis
  • 5S, 5,8S, 18S, and 28S rRNA
    • 18S rRNA: component of the small subunit of ribosomes (40S)
    • 5S, 5,8S, and 28SrRNA: components of the large subunit of ribosomes (60S)
      • 28S rRNA catalyzes the formation of peptide bonds in the ribosome (often referred to as a ribozyme)
snRNA (small nuclear RNA
  • Class of noncoding RNAs in the nucleus
  • Component of the spliceosome
  • Involved in the splicing of pre-mRNA
snoRNA (small nucleolar RNA)
  • Class of noncoding RNAs in the nucleolus
  • Modifying RNA molecules, especially rRNAs including through methylation of ribose residues
RNA component of signal recognition particles
or 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)
  • In humans, the matrix sequence is 5'-UAACCCUA-3'
  • Composed of 451 nucleotides and does not have a poly(A) tail
miRNA (microRNA)
  • Class of regulatory, noncoding RNAs
  • Encoded in introns
  • Regulate gene expression by binding the 3' untranslated region of certain mRNA to prevent translation or ensure degradation
    • Dysfunctional miRNA expression may contribute to the development of some cancers (e.g., an 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
  • Used experimentally or arise in viral infections, i.e., are introduced into the cell or organism and regulate gene expression (bind complementary mRNAs and ensure their degradation)
  • Composed of ∼ 20–30 nucleotides
  • Formed from double-stranded precursor molecules from a similar mechanism as for miRNA

last updated 04/18/2018
{{uncollapseSections(['vLcAz10', 'wLch-10', '9LcN-10', 'DLc1-10', 'CLcq-10', 'xLcE-10'])}}