Molecular Development - Protein: Difference between revisions

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'''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)
'''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)


{|class="wikitable sortable"
{{Amino Acid Table}}
!Amino Acid
!3-Letter
!1-Letter
!Side chain polarity
!Side chain acidity or basicity of neutral species
!Hydropathy index
<ref name="PMID7108955"><pubmed>7108955</pubmed></ref>
|-align="center"
|[[#Alanine|Alanine]]
|Ala
|A
|nonpolar
|neutral
|<span style="color:orange;">1.8</span>
|-align="center"
|[[#Arginine|Arginine]]
|Arg
|R
|polar
|basic (strongly)
|<span style="color:blue;">-4.5</span>
|-align="center"
|[[#Asparagine|Asparagine]]
|Asn
|N
|polar
|neutral
|<span style="color:blue;">-3.5</span>
|-align="center"
|[[#Aspartic acid|Aspartic acid]]
|Asp
|D
|polar
|acidic
|<span style="color:blue;">-3.5</span>
|-align="center"
|[[#Cysteine|Cysteine]]
|Cys
|C
|polar
|neutral
|<span style="color:orange;">2.5</span>
|-align="center"
|[[#Glutamic acid|Glutamic acid]]
|Glu
|E
|polar
|acidic
|<span style="color:blue;">-3.5</span>
|-align="center"
|[[#Glutamine|Glutamine]]
|Gln
|Q
|polar
|neutral
|<span style="color:blue;">-3.5</span>
|-align="center"
|[[#Glycine|Glycine]]
|Gly
|G
|nonpolar
|neutral
|<span style="color:orange;">-0.4</span>
|-align="center"
|[[#Histidine|Histidine]]
|His
|H
|polar
|basic (weakly)
|<span style="color:blue;">-3.2</span>
|-align="center"
|[[#Isoleucine|Isoleucine]]
|Ile
|I
|nonpolar
|neutral
|<span style="color:orange;">4.5</span>
|-align="center"
|[[#Leucine|Leucine]]
|Leu
|L
|nonpolar
|neutral
|<span style="color:orange;">3.8</span>
|-align="center"
|[[#Lysine|Lysine]]
|Lys
|K
|polar
|basic
|<span style="color:blue;">-3.9</span>
|-align="center"
|[[#Methionine|Methionine]]
|Met
|M
|nonpolar
|neutral
|<span style="color:orange;">1.9</span>
|-align="center"
|[[#Phenylalanine|Phenylalanine]]
|Phe
|F
|nonpolar
|neutral
|<span style="color:orange;">2.8</span>
|-align="center"
|[[#Proline|Proline]]
|Pro
|P
|nonpolar
|neutral
|<span style="color:orange;">-1.6</span>
|-align="center"
|[[#Serine|Serine]]
|Ser
|S
|polar
|neutral
|<span style="color:blue;">-0.8</span>
|-align="center"
|[[#Threonine|Threonine]]
|Thr
|T
|polar
|neutral
|<span style="color:blue;">-0.7</span>
|-align="center"
|[[#Tryptophan|Tryptophan]]
|Trp
|W
|nonpolar
|neutral
|<span style="color:orange;">-0.9</span>
|-align="center"
|[[#Tyrosine|Tyrosine]]
|Tyr
|Y
|polar
|neutral
|<span style="color:orange;">-1.3</span>
|-align="center"
|[[#Valine|Valine]]
|Val
|V
|nonpolar
|neutral
|<span style="color:orange;">4.2</span>
|}


'''Hydropathy Index'''<ref name="PMID7108955"><pubmed>7108955</pubmed></ref>
'''Hydropathy Index'''<ref name="PMID7108955"><pubmed>7108955</pubmed></ref>
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===Class, amino acid, R group===
===Class, amino acid, R group===
====Acidic====
====Acidic====
:D Asp [[Aspartic acid]] -CH2-COOH where both the O and the OH are bonded to the C
:D Asp [[Molecular_Development_-_Protein#Aspartic acid|Aspartic acid]] -CH2-COOH where both the O and the OH are bonded to the C
:E Glu [[Glutamic acid]] -CH2-CH2-COOH
:E Glu [[Molecular_Development_-_Protein#Glutamic acid|Glutamic acid]] -CH2-CH2-COOH


====Basic====
====Basic====
:K Lys [[Lysine]] -CH2-CH2-CH2-CH2-NH3+
:K Lys [[Molecular_Development_-_Protein#Lysine|Lysine]] -CH2-CH2-CH2-CH2-NH3+
:R Arg [[Arginine]] -CH2-CH2-CH2-NH-C-(NH2)2 &nbsp;:where 2 NH2 groups are attached to the final C
:R Arg [[Molecular_Development_-_Protein#Arginine|Arginine]] -CH2-CH2-CH2-NH-C-(NH2)2 &nbsp;:where 2 NH2 groups are attached to the final C
:H His [[Histidine]] -CH2-&lt;C-HN-HC=NH+-HC=&gt; &nbsp;:where &lt; chain &gt; actually forms a pentagonal ring bonded at the C
:H His [[Molecular_Development_-_Protein#Histidine|Histidine]] -CH2-&lt;C-HN-HC=NH+-HC=&gt; &nbsp;:where &lt; chain &gt; actually forms a pentagonal ring bonded at the C


====Uncharged Polar====
====Uncharged Polar====
:S Ser [[Serine]] -CH2-OH
:S Ser [[Molecular_Development_-_Protein#Serine|Serine]] -CH2-OH
:T Thr [[Threonine]] -CH-CH3OH &nbsp;:where both the CH3 and the OH attach at the initial CH
:T Thr [[Molecular_Development_-_Protein#Threonine|Threonine]] -CH-CH3OH &nbsp;:where both the CH3 and the OH attach at the initial CH
:Y Tyr [[Tyrosine]] -CH2-&lt;CH=CH-CH=COH-CH=CH-&gt; &nbsp;:where &lt; ... &gt; forms a hexagonal ring with the OH at the far end
:Y Tyr [[Molecular_Development_-_Protein#Tyrosine|Tyrosine]] -CH2-&lt;CH=CH-CH=COH-CH=CH-&gt; &nbsp;:where &lt; ... &gt; forms a hexagonal ring with the OH at the far end
:N Asn [[Asparagine]] -CH2-CONH2 &nbsp;:where both the =O and the -NH2 attach to the C
:N Asn [[Molecular_Development_-_Protein#Asparagine|Asparagine]] -CH2-CONH2 &nbsp;:where both the =O and the -NH2 attach to the C
:O Gln [[Glutamine]] -CH2-CH2-CONH2 &nbsp;:same as Asparagine but with an extra CH2<br />
:O Gln [[Molecular_Development_-_Protein#Glutamine|Glutamine]] -CH2-CH2-CONH2 &nbsp;:same as Asparagine but with an extra CH2<br />
C Cys [[Cysteine]] -CH2-S-H
C Cys [[Molecular_Development_-_Protein#Cysteine|Cysteine]] -CH2-S-H


====Non-Polar====
====Non-Polar====
:G Gly [[Glycine]] -H
:G Gly [[Molecular_Development_-_Protein#Glycine|Glycine]] -H
:A Ala [[Alanine]] -CH3
:A Ala [[Molecular_Development_-_Protein#Alanine|Alanine]] -CH3
:V Val [[Valine]] -CH-(CH3)2
:V Val [[Molecular_Development_-_Protein#Valine|Valine]] -CH-(CH3)2
:L Leu [[Leucine]] -CH2-CH-(CH3)2
:L Leu [[Molecular_Development_-_Protein#Leucine|Leucine]] -CH2-CH-(CH3)2
:I Ile [[Isoleucine]] -CH-(CH3, CH2-CH3)
:I Ile [[Molecular_Development_-_Protein#Isoleucine|Isoleucine]] -CH-(CH3, CH2-CH3)
:P Pro [[Proline]] -&lt;CH2-CH2-CH2&gt; &nbsp;:where the other end of the ring attaches at the N by replacing an H
:P Pro [[Molecular_Development_-_Protein#Proline|Proline]] -&lt;CH2-CH2-CH2&gt; &nbsp;:where the other end of the ring attaches at the N by replacing an H
:F Phe [[Phenylalanine]] -CH2-&lt;CH=CH-CH=CH-CH=CH-&gt; &nbsp;:like tyrosine without the OH at the far end of the ring.
:F Phe [[Molecular_Development_-_Protein#Phenylalanine|Phenylalanine]] -CH2-&lt;CH=CH-CH=CH-CH=CH-&gt; &nbsp;:like tyrosine without the OH at the far end of the ring.
:M Met [[Methionine]] -CH2-CH2-S-CH3
:M Met [[Molecular_Development_-_Protein#Methionine|Methionine]] -CH2-CH2-S-CH3
:W Trp [[Tryptophan]] -CH2-&lt;pentagonal ring with NH&gt;&lt;Hexagonal Phenyl ring&gt;
:W Trp [[Molecular_Development_-_Protein#Tryptophan|Tryptophan]] -CH2-&lt;pentagonal ring with NH&gt;&lt;Hexagonal Phenyl ring&gt;
 
===About Amino Acids===
 
* A strong Disulphide (Disulfide) Bridge (S-S) sometimes can be created between the sulfur in the side chains in two [[#Cysteine|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==
==Amino Acids==


===Arginine===
===Arginine===
 
(R Arg)
* basic amino acid
* -CH2-CH2-CH2-NH-C-(NH2)2 &nbsp;:where 2 NH2 groups are attached to the final C


===Alanine===
===Alanine===
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===Cysteine===
===Cysteine===
(Cys)
(Cys)
* 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===
===Aspartic Acid===
(Asp)
(D, Asp)
* Acidic amino acid
* -CH2-COOH where both the O and the OH are bonded to the C.
 
===Glutamic Acid===
===Glutamic Acid===
(Glu)
(E, Glu)
 
* Acidic amino acid
* -CH2-CH2-COOH
 
===Phenylalanine===
===Phenylalanine===
(Phe)
(Phe)
Line 219: Line 91:
(Gly)
(Gly)
===Histidine===
===Histidine===
(His)
(H, His)
* basic amino acid
* -CH2-&lt;C-HN-HC=NH+-HC=&gt; &nbsp;:where &lt; chain &gt; actually forms a pentagonal ring bonded at the C
 
===Isoleucine===
===Isoleucine===
(Ile)
(Ile)
===Lysine===
===Lysine===
(Lys)
(K, Lys)
* basic amino acid
* -CH2-CH2-CH2-CH2-NH3+
 
===Leucine===
===Leucine===
(Leu)
(Leu)

Latest revision as of 07:15, 29 March 2012

Introduction

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

Protein

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

[1]

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

Acidic

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

Basic

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

Non-Polar

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

Arginine

(R Arg)

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

Alanine

(Ala)

Cysteine

(Cys)

  • 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

Phenylalanine

(Phe)

Glycine

(Gly)

Histidine

(H, His)

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

Isoleucine

(Ile)

Lysine

(K, Lys)

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

Leucine

(Leu)

Methionine

(Met)

Asparagine

(Asn)

Proline

(Pro)

Glutamine

(Gln)

Arginine

(Arg)

Serine

(Ser)

Threonine

(Thr)

Valine

(Val)

Tryptophan

(Trp)

Tyrosine

(Tyr)

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.

References

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


External Links

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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, March 28) Embryology Molecular Development - Protein. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Molecular_Development_-_Protein

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