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EBI 2Can Basic Biology

Basic Biology - Molecules of life - Small Molecules

This page contains general information about the small molecules of life, primarily amino acids and nucleotides. These molecules are the building blocks of proteins and DNA/RNA respectively.

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Amino Acids Abbreviation Table



The one-letter and the three-letter codes, which have been used to represent polypeptide sequences since the mid 1960's, were defined by the IUPAC and IUBMB in 1983. The following table lists the amino acids and there corresponding one-letter and three-letter code abbreviations.
  • Click here to see detailed structures of the amino acids.
  • Click here to see a summarised schematic of all the amino acids.
  • Click here to see a more detailed analysis of amino acid properties.
  • Click here to see a 3D animations of amino acids.

Standard Encoded Amino Acids
A Ala alanine M Met methionine
C Cys cysteine N Asn asparagine ("asparagiNe", "aspartic-NH2")
D Asp aspartic acid ("asparDic acid") P Pro proline
E Glu glutamic acid ("gluEtamic acid") Q Gln glutamine ("Qutamine")
F Phe phenylalanine ("Fenylalanine") R Arg arginine ("aRginine")
G Gly glycine S Ser serine
H His histidine T Thr threonine
I Ile isoleucine V Val valine
K Lys lysine ("K" next to "L") W Trp tryptophan ("tWiptophan", or double-ring)
L Leu leucine Y Tyr tyrosine ("tYrosine")
Amino Acid Ambiguities
B Asx aspartic acid or asparagine ("B" near "D", uncertain result of hydrolysis)
J Xle leucine or isoleucine ("J" between "I" and "L", uncertain result of mass-spec)
X Xaa unknown or unspecified amino acid ("Unk" is sometimes used as an abbreviation)
Z Glx glutamic acid or glutamine ("Z" near "X", uncertain result of hydrolysis)
Special Encoded Amino Acids
U Sec selenocysteine (the UniProt Knowledgebase uses "C" and a feature rather than "U")
O Pyl pyrrolysine ("pyrrOlysine", the UniProt Knowledgebase uses "K" and a feature rather than "O")



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Amino Acid Properties and Substitutions



A substitution is more likely to occur between amino acids with similar biochemical properties. For example the hydrophobic amino acids Isoleucine(I) and valine(V) are more likely to substitute for one another than the hydrophilic amino acid cystine would with one of these. Amino acids come in the following types.

  • Click here to see detailed structures of the amino acids.
  • Click here to see a summarised schematic of all the amino acids.
  • Click here to see a more detailed analysis of amino acid properties.
  • Click here to see a 3D animations of amino acids.

Type of
Amino Acid		 Properties
(at physiological pH)		 Amino Acids
Amino acids with aliphatic hydrophobic side chains
 The hydrophobic side chains of these amino acids will not form hydrogen bonds or ionic bonds with other groups. These hydrophobic amino acids tend to be buried in the centre of proteins away from the surrounding aqueous environment.
 Ala, Val, Leu, lle, Met, Pro, Phe, Trp.
Amino acids with uncharged but polar side chains
 The side chains of these amino acids are uncharged.
Gly, Ser, Tyr, Asn, Gln, Cys.
Amino acids with acidic side chains
 These have a carboxylic acid group in their side chain and are very hydrophilic.
 Asp, Glu.
Amino acids with basic side chains
 The positive charge on these side chains makes them hydrophilic and they are likely to be found at the protein surface
 Lys, Arg, His.

Courtesy of http://prowl.rockefeller.edu


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DNA/RNA (Nucleotide) Sequences



Nucleotide bases fall into two categories depending on the ring structure of the base. Purines (Adenine and Guanine) are two ring bases, pyrimidines (Cytosine and Thymine) are single ring bases. Bases form pairs, these pairs combine a purine base with a pyrimidine base. These pairs are: CG, AT in the case of DNA and AU in RNA.

One-letter code Name Location
A Adenine DNA/RNA
G Guanine
DNA/RNA
C Cytosine
DNA/RNA
T Thymine
DNA
U Uracil RNA



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Image

Table of Standard Genetic Code



The genetic code in the table above has also been called "The Universal Genetic Code". It is known as "universal", because it is used by all known organisms as a code for DNA, mRNA, and tRNA. The universality of the genetic code encompases animals (including humans), plants, fungi, archaea, bacteria, and viruses. However, all rules have their exceptions, and such is the case with the genetic code; small variations in the code exist in mitochondria and certain microbes. Nonetheless, it should be emphasised that these variances represent only a small fraction of known cases, and that the genetic code applies quite broadly, certainly to all known nuclear genes.

    Second Position of Codon    
    T C A G    
F
i
r
s
t

P
o
s
i
t
i
o
n		 T
TTT Phe [F]
TTC Phe [F]
TTA Leu [L]
TTG Leu [L]
TCT Ser [S]
TCC Ser [S]
TCA Ser [S]
TCG Ser [S]
TAT Tyr [Y]
TAC Tyr [Y]
TAA Ter [end]
TAG Ter [end]
TGT Cys [C]
TGC Cys [C]
TGA Ter [end]
TGG Trp [W]
T
C
A
G
T
h
i
r
d

P
o
s
i
t
i
o
n
C
CTT Leu [L]
CTC Leu [L]
CTA Leu [L]
CTG Leu [L]
CCT Pro [P]
CCC Pro [P]
CCA Pro [P]
CCG Pro [P]
CAT His [H]
CAC His [H]
CAA Gln [Q]
CAG Gln [Q]
CGT Arg [R]
CGC Arg [R]
CGA Arg [R]
CGG Arg [R]
T
C
A
G
A
ATT Ile [I]
ATC Ile [I]
ATA Ile [I]
ATG Met [M]
ACT Thr [T]
ACC Thr [T]
ACA Thr [T]
ACG Thr [T]
AAT Asn [N]
AAC Asn [N]
AAA Lys [K]
AAG Lys [K]
AGT Ser [S]
AGC Ser [S]
AGA Arg [R]
AGG Arg [R]
T
C
A
G
G
GTT Val [V]
GTC Val [V]
GTA Val [V]
GTG Val [V]
GCT Ala [A]
GCC Ala [A]
GCA Ala [A]
GCG Ala [A]
GAT Asp [D]
GAC Asp [D]
GAA Glu [E]
GAG Glu [E]
GGT Gly [G]
GGC Gly [G]
GGA Gly [G]
GGG Gly [G]
T
C
A
G





The four basic types of molecules involved in life
Small Molecules | Proteins | DNA | RNA

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