Molecular Development - Protein

From Embryology


Gene expression can often simply be described by the pathway: DNA -> mRNA -> Protein.

While each cell contains the same genetic material, not all genes are ever expressed and the subset of genes expressed at any one time affects cellular differentiation and mature cell function. This can be impacted by both signaling and epigenetic mechanisms. This page provides basic information about the building blocks of all proteins, the amino acids.

Molecular Links: molecular | genetics | epigenetics | mitosis | meiosis | X Inactivation | Signaling | Factors | Mouse Knockout | microRNA | Mechanisms | Developmental Enhancers | Protein | Genetic Abnormal | Category:Molecular
Factor Links: AMH | hCG | BMP | sonic hedgehog | bHLH | HOX | FGF | FOX | Hippo | LIM | Nanog | NGF | Nodal | Notch | PAX | retinoic acid | SIX | Slit2/Robo1 | SOX | TBX | TGF-beta | VEGF | WNT | Category:Molecular


The individual amino acids that form all proteins can be represented by a standardised single letter code, or three letter code or by their entire name.

Single Letter Code

A - Alanine (Ala) | C - Cysteine (Cys) | D - Aspartic Acid (Asp) | E - Glutamic Acid (Glu) | F - Phenylalanine (Phe) | G - Glycine (Gly) | H - Histidine (His) | I - Isoleucine (Ile) | K - Lysine (Lys) |L - Leucine (Leu) | M - Methionine (Met) | N - Asparagine (Asn) | P - Proline (Pro) | Q - Glutamine (Gln) | R - Arginine (Arg) | S - Serine (Ser) | T - Threonine (Thr) | V - Valine (Val) | W - Tryptophan (Trp) | Y - Tyrosine (Tyr)

Amino Acid 3-Letter 1-Letter Side chain polarity Side chain acidity or basicity of neutral species Hydropathy index


Alanine Ala A nonpolar neutral 1.8
Arginine Arg R polar basic (strongly) -4.5
Asparagine Asn N polar neutral -3.5
Aspartic acid Asp D polar acidic -3.5
Cysteine Cys C polar neutral 2.5
Glutamic acid Glu E polar acidic -3.5
Glutamine Gln Q polar neutral -3.5
Glycine Gly G nonpolar neutral -0.4
Histidine His H polar basic (weakly) -3.2
Isoleucine Ile I nonpolar neutral 4.5
Leucine Leu L nonpolar neutral 3.8
Lysine Lys K polar basic -3.9
Methionine Met M nonpolar neutral 1.9
Phenylalanine Phe F nonpolar neutral 2.8
Proline Pro P nonpolar neutral -1.6
Serine Ser S polar neutral -0.8
Threonine Thr T polar neutral -0.7
Tryptophan Trp W nonpolar neutral -0.9
Tyrosine Tyr Y polar neutral -1.3
Valine Val V nonpolar neutral 4.2

Hydropathy Index[1]

  • a number representing the hydrophobic or hydrophilic properties of the amino acid sidechain.
  • larger the number the more hydrophobic the amino acid.
  • most hydrophobic amino acids are isoleucine (4.5) and valine (4.2), hydrophobic amino acids tend to be internal
  • most hydrophilic amino acids are arginine (-4.5) and lysine (-3.9), hydrophilic amino acids are more commonly found towards the protein surface.

Class, amino acid, R group


D Asp Aspartic acid -CH2-COOH where both the O and the OH are bonded to the C
E Glu Glutamic acid -CH2-CH2-COOH


K Lys Lysine -CH2-CH2-CH2-CH2-NH3+
R Arg Arginine -CH2-CH2-CH2-NH-C-(NH2)2  :where 2 NH2 groups are attached to the final C
H His Histidine -CH2-<C-HN-HC=NH+-HC=>  :where < chain > actually forms a pentagonal ring bonded at the C

Uncharged Polar

S Ser Serine -CH2-OH
T Thr Threonine -CH-CH3OH  :where both the CH3 and the OH attach at the initial CH
Y Tyr Tyrosine -CH2-<CH=CH-CH=COH-CH=CH->  :where < ... > forms a hexagonal ring with the OH at the far end
N Asn Asparagine -CH2-CONH2  :where both the =O and the -NH2 attach to the C
O Gln Glutamine -CH2-CH2-CONH2  :same as Asparagine but with an extra CH2

C Cys Cysteine -CH2-S-H


G Gly Glycine -H
A Ala Alanine -CH3
V Val Valine -CH-(CH3)2
L Leu Leucine -CH2-CH-(CH3)2
I Ile Isoleucine -CH-(CH3, CH2-CH3)
P Pro Proline -<CH2-CH2-CH2>  :where the other end of the ring attaches at the N by replacing an H
F Phe Phenylalanine -CH2-<CH=CH-CH=CH-CH=CH->  :like tyrosine without the OH at the far end of the ring.
M Met Methionine -CH2-CH2-S-CH3
W Trp Tryptophan -CH2-<pentagonal ring with NH><Hexagonal Phenyl ring>

About Amino Acids

  • A strong Disulphide (Disulfide) Bridge (S-S) sometimes can be created between the sulfur in the side chains in two Cysteine amino acids. This plays a strong role in forming the 3 dimensional protein structure.
  • Additional bonds occur between acidic and basic end groups of the side chains.
  • Polar side groups like to remain in a polar environment such as the water surrounding the protein.
  • A protein is most stable when in its lowest energy configuration.

Amino Acids


(R Arg)

  • basic amino acid
  • -CH2-CH2-CH2-NH-C-(NH2)2  :where 2 NH2 groups are attached to the final C





  • A strong Disulphide (Disulfide) Bridge (S-S) sometimes can be created between the sulfur in the side chains in two Cysteine amino acids.
  • This plays a strong role in forming the folded 3 dimensional protein structure.

Aspartic Acid

(D, Asp)

  • Acidic amino acid
  • -CH2-COOH where both the O and the OH are bonded to the C.

Glutamic Acid

(E, Glu)

  • Acidic amino acid
  • -CH2-CH2-COOH






(H, His)

  • basic amino acid
  • -CH2-<C-HN-HC=NH+-HC=>  :where < chain > actually forms a pentagonal ring bonded at the C




(K, Lys)

  • basic amino acid
  • -CH2-CH2-CH2-CH2-NH3+























Molecular Development - Starting Out

Model of Sonic hedgehog signaling in the drosophila wing

There are several different ways to begin to look at molecular development.

  • look at the earliest molecular events involved in patterning the differentiation of cells- axis formation.
  • or look at early events in patterning with differentiation and migration of cells to form the trilaminar embryo (gastrulation).
  • or look at the signaling mechanisms and the different types of factors involved.
  • or look at their role in the development of specific systems.

Signaling during development, though complex, can also be grouped into a few specific classes. These mechanisms have also been listed and described briefly on Signaling Mechanisms page.

For this section, Molecular Biology of the Cell (now indexed and available online from PubMed) and the extracted Cell Biology version are good reference texts. Also the key journals in this area are: Development, Genes and Development, PNAS, EMBOJ.

There is also detailed molecular information available from the abnormalities (page 2 of each section of notes) where there are links to the OMIM Database entry for specific genetic disorders.

Please understand that these notes are a new addition and are therefore under constant revision.


  1. 1.0 1.1 <pubmed>7108955</pubmed>

External Links

External Links Notice - The dynamic nature of the internet may mean that some of these listed links may no longer function. If the link no longer works search the web with the link text or name. Links to any external commercial sites are provided for information purposes only and should never be considered an endorsement. UNSW Embryology is provided as an educational resource with no clinical information or commercial affiliation.

Glossary Links

Glossary: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | Numbers | Symbols | Term Link

Cite this page: Hill, M.A. (2024, April 22) Embryology Molecular Development - Protein. Retrieved from

What Links Here?
© Dr Mark Hill 2024, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G