Nucleic Acids

Nucleic acids are polymers of nucleotides, organic molecules composed of a sugar, a phosphate group, and a nitrogenous base. Nucleic acids are responsible for storage, replication, and expression of genetic information. They are “acids” because of the phosphate groups that are acidic in nature and “nucleic” because they are stored in the cell’s nucleus. The 2 nucleic acids most commonly seen in eukaryotic cells are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Though chemically similar, DNA and RNA have specific biological functions to which their respective structures are tailored.

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Overview

Definition

Nucleic acids are polymers of nucleotides. Main classes:

  • Deoxyribonucleic acid (DNA
  • Ribonucleic acid (RNA)

Nucleotide

Nucleotides are the basic units of a nucleic acid.

Composed of:

  • 5-carbon sugar
  • Nitrogenous base 
  • Phosphate group

5-carbon sugar:

  • Distinguishing factor between DNA and RNA: 
    • Ribose in RNA versus deoxyribose in DNA
    • The 2’ carbon is bound to a hydroxyl (OH) in RNA or a hydrogen (H) in DNA.
  • The 5’ carbon is bound to a phosphate group (PO4).
  • The 1’ carbon is bound to a nitrogenous base:
    • Adenine (A)
    • Guanine (G) 
    • Thymine (T) 
    • Cytosine (C)
    • Uracil (U)

Nitrogenous bases:

  • Purines: adenine and guanine (2-ring structures)
  • Pyrimidines: cytosine, thymine, and uracil (single-ring structures)
  • Complementary base pairing: Within nucleic acid polymers, purine bases pair exclusively with their complementary pyrimidine bases. 
    • DNA: Adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).
    • RNA: Adenine (A) pairs with thymine (U), and guanine (G) pairs with cytosine (C).
    • A-T bases held together by 2 H bonds
    • G-C bases held together by 3 H bonds

Nucleotides are assembled into nucleic acid polymers by adding 5’–3’ phosphodiester bonds:

  • Condensation reaction between the OH group on the 5’ carbon of 1 nucleotide and the H on the 3’ carbon from the next nucleotide 
  • Creates nucleotide chains with a free 5’ phosphate and 3’ OH to continue synthesis

Naming nucleotides:

  • Nucleoside monophosphate (e.g., adenosine monophosphate (AMP)): a nucleoside (organic base and pentose) and 1 phosphate group
  • Nucleoside diphosphate (e.g., adenosine diphosphate (ADP)): a nucleoside (organic base and pentose) and 2 phosphate groups
  • Nucleoside triphosphate (e.g., adenosine triphosphate (ATP)): a nucleoside (organic base and pentose) and 3 phosphate groups
  • For DNA, add “deoxy” to the base name (deoxyadenosine triphosphate).

DNA

Overview

DNA is the genetic blueprint for life, containing codes for genes.

  • Double-stranded helix (Watson and Crick) strands are complementary and antiparallel:
    • 5’–3’ (sense) strand
    • 3’–5’ (antisense) strand
    • The most common are B-DNA (right-handed helix), Z-DNA (left-handed helix), and A-DNA (compact helix), which are not found in cells.
  • Strands held to each other by:
    • Hydrogen bonds
    • Van der Waals forces
    • Hydrophobic interaction between base pairs
  • Chargaff’s rule: 
    • Due to complementary base pairing
    • In DNA, the number of A should equal T, G = C, and A + G = T + C.

Organization

  • In eukaryotes: found in nucleus and mitochondria as chromosomes 
    • In humans: 46 homologous chromosomes (23 pairs)
    • Coding information contained within segments of chromosomes called genes
  • In prokaryotes: free-floating as chromosome or plasmid 
  • DNA → nucleosome (DNA + histone octamer) → solenoid → chromatin → chromosome
  • Euchromatin: 
    • Less condensed
    • More transcription (TX)
    • Metabolically active cells
  • Heterochromatin:
    • More condensed
    • Low TX
    • Cells with low metabolic activity
  • Histone modification: affect access to DNA and thus TX 
    • Acetylation (increases TX)
    • Methylation (increases or decreases TX, epigenetics →  heritable)
    • Phosphorylation (increases or decreases TX)
    • Ubiquitylation
    • ADP-ribosylation

Mitochondrial DNA (mtDNA)

  • 1% of cellular DNA
  • Inherited only from the mother (non-Mendelian inheritance)
  • Characteristics of human mtDNA:
    • Circular, double-stranded, composed of heavy (H) and light (L) strands
    • Contains 16,569 base pairs
    • Encodes ribosomal RNAs, transfer RNAs (tRNAs), and protein subunits necessary for oxidative phosphorylation (ATP production)
    • High mutation rate (5–10 times that of nuclear DNA)
  • Presence of mtDNA led to theory of endosymbiosis of mitochondria: 
    • Once free-living prokaryotic microbes
    • Engulfed by host cell and became organelles
    • Circular DNA
    • Replication by binary fission

RNA

RNA: protein biosynthesis, regulatory functions, processing, and transport

  • Thymine replaced by uracil
  • Single stranded (most of the time)
  • Phosphate sugar backbone with nucleotides hanging off

Different forms of RNA exist for specialized purposes for the phases of replication and translation of genetic material:

  • Transcription:
    • Heterogeneous nuclear RNA (hnRNA, or pre-mRNA): nuclear precursor to messenger RNA (mRNA)
    • mRNA: codes for proteins; complement to DNA strand; serves as template for translation; transported from nucleus to cytosol
  • Translation:
    • tRNA: non-coding; adaptor molecule that translates mRNA codons into amino acids; contains anticodon and amino acid; contains thymine
    • Ribosomal RNA (rRNA): non-coding; bound to proteins to make ribosomal subunits; catalyzes protein biosynthesis in ribosomes; dominant form of RNA
  • Regulatory functions:
    • Small interfering RNA (siRNA): non-coding; binds to mRNA complement to signal cellular degradation
    • MicroRNA (miRNA): non-coding; binds to mRNA complement to inhibit translation
  • Processing and transport:
    • Small nuclear RNA (snRNA): forms a spliceosome (with other proteins) to splice mRNA
    • Small nucleolar RNA (snoRNA): guides modification of snRNA and rRNA
    • Small conditional RNA (scRNA): part of a complex that guides proteins to be exported to extracellular space
  • Mitochondrial RNA (mtRNA): mitochondrial mRNA, rRNA, and tRNA that function similar to eukaryotic versions
Transcription Nucleic-acids

Structures of RNA and DNA

Image by Lecturio. License: CC BY-NC-SA 4.0

References

  1. Weil, PA. (2018). Nucleic acid structure & function. In VW Rodwell, DA Bender, KM Botham, PJ Kennelly & PA Weil (Eds.), Harper’s illustrated biochemistry, 31e (). New York, NY: McGraw-Hill Education. Retrieved May 17, 2021, from accessmedicine.mhmedical.com/content.aspx?aid=1160190679

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