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Nucleic Acids and Proteins
Modern Linguistics for the Genomics and Bioinformatics Era
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GENOME
↕
CHROMOSOME
↕
GENE
↕
DNA
↕
NUCLEOTIDE
Fig. 1. Simple organizational
hierarchy of genetic material.
GENOME (1)
↕
CHROMOSOME (23)
↕
DNA (23)
↕
GENE (~30,000)
↕
NUCLEOTIDE (3 × 109)
Fig. 2. Numerically annotated
hierarchy of genetic material.
Fig. 3. Molecular structure of nucleotides, the building blocks of DNA and RNA. The 1' Æ 5' numbering convention used to designate carbons in the deoxyribose and ribose sugars is annotated only on
the deoxyribose sugar. “B” extending from the 1' carbon of deoxyribo- and ribonucleotides represent
the purine and pyrimidine nitrogenous bases. Designation of the different phosphate groups (a, b, g)
are depicted on the deoxyribose nucleotide.
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Fig. 4. Molecular structure of the tetranucleotide GTAG. The H present at 2' carbon of each sugar
indicates that this is a DNA chain composed of deoxynucleotides. Phosphates involved in cementing
adjacent nucleotides together with a phosphodiester bond are shown in red (on CD). A single free, 5'
phosphate is pictured in blue. A free 3'-OH group at the opposite end of the chain is also depicted in
blue.
Fig. 5. Complementarity between specific nitrogenous bases. Pictured are the A-T and G-C base pairs
present in a DNA double helix. (- - - -) represent hydrogen bonds between participating atoms. A
purine juxtaposed with a pyrimidine after hydrogen bond formation generates a dimension of 20
angstroms, the width of a DNA double helix.
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Fig. 6. Base pair complementarity is the basis for faithful duplication of the double helix. Chains of
a DNA helix are pictured in an antiparallel configuration. Horizontal lines between the complementing bases denote hydrogen bonds (see Fig. 4). DNA polymerase (oval) polymerizes DNA in a
5' to 3' in an antiparallel direction on each strand. Each new daughter helix is composed of an
original stand and a newly synthesized chain, indicative of semi-conservative replication.
Fig. 7. A transfer RNA (tRNA) molecule acting as an interpreter between the language of nucleic
acids (DNA and RNA) and the language of amino acids (proteins). A tRNA, pictured as a polymer of
76 individual ribonucleotides (individual squares), is folded into the universal cloverleaf structure
by virtue of intra-molecular hydrogen bonding between complementing bases. The black dots denote base-pairing by hydrogen bonds to form stems. Gray squares are unpaired nucleotides, forming loops. The triplet anticodon nucleotides (34–36) are shown recognizing and interacting via
hydrogen bonding with the appropriate triplet codon within an mRNA molecule.
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Fig. 8. Molecular structure of the 20 amino acid side-chains (R-groups), listed according to chemical character (A, polar or B, charged). Beneath each structure is the name of the R-group, is threeletter designation, and its single letter designation. In an amino acid, the individual side-chain is
attached to by a covalent bond to the common backbone NH2 -CH-COOH, where C indicates the
position of attachment.
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Table 1
Universal Genetic Code
First
Second
Third
5'
U
C
A
G
3'
U
Phe
Phe
Leu
Leu
Ser
Ser
Ser
Ser
Tyr
Tyr
Tyr
Tyr
Cys
Cys
Stop
Trp
U
C
A
G
C
Leu
Leu
Leu
Leu
Pro
Pro
Pro
Pro
His
His
Gln
Gln
Arg
Arg
Arg
Arg
U
C
A
G
A
Ile
Ile
Ile
Met
Thr
Thr
Thr
Thr
Asn
Asn
Lys
Lys
Ser
Ser
Arg
Arg
U
C
A
G
G
Val
Val
Val
Val
Ala
Ala
Ala
Ala
Asp
Asp
Glu
Glu
Gly
Gly
Gly
Gly
U
C
A
G
Fig. 9. Membrane proteins: An example of how amino acid distribution dictates structure and function. Pictured in black are phospholipids that create the hydrophobic interior of a lipid bi-layer
membrane. Small darker dots indicate nonpolar, hydrophobic amino acid constituents of a polypeptide chain. Small lighter dots represent polar, charged, amino acid residues that are capable of
interacting with the aqueous, hydrophilic environments on either side of the cell membrane. Such
trans-membrane protein domains typify proteins that serve as channels and as receptors to perceive external stimuli.
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