Proteopedia - User contributions [en]

Proteins: primary and secondary structure

2021-12-08T18:35:40Z

Meghan Wright: grammar and spelling

[[es:Proteins: primary and secondary structure (Spanish)]]
[[hi:Proteins: primary and secondary structure (Hindi)]]

<StructureSection load='' size='500' side='right' caption='' scene='60/603296/Primaria/2'>
<big>
*'''Primary structure'''
:*In this <scene name='60/603296/Primaria/2'>initial view</scene> we can see a short fragment of a polypeptide chain in order to analyze some features of its ''primary structure''. Atoms forming the chain ''backbone'' are disposed in zig-zag, as required by geometry of its bonding orbitals. Side chains of amino acid residues (or R groups) protrude outwards either side of backbone.
:*Let's go now to a <scene name='60/603296/Primaria3/1'>peptide bond</scene> between two amino acid residues. Because phenomenon of resonance, peptide bond shows some features of a double bond, which prevents free rotation of atoms on either bond side. So, six atoms marked in <scene name='60/603296/Primaria3/7'>rectangle</scene> on model window are always confined to the same rigid flat. We can test it by <scene name='60/603296/Primaria3/6'>activate rotation</scene>.
:*Polypeptide chain backbone consist in a monotonous succession in wich the following sequenze repeats: <scene name='60/603296/Primaria3/8'>alpha carbon</scene>, <scene name='60/603296/Primaria3/9'>carboxyl group carbon</scene>, <scene name='60/603296/Primaria3/11'>amino group nitrogen</scene>. Minding the restrictions to free rotation in ''peptide bond'', we can visualize the polypeptide chain as a succession of <scene name='60/603296/Primaria3/12'>rigid flats</scene>. Each of these rigid flats can freely rotate respect each other.

*'''Secondary structure'''.- In most proteins there are two main types of secondary structure.
:*<scene name='60/603296/Secundaria/4'>Alpha helix</scene>.- It is a helical structure with a thread pitch of 0.56 nm. Let's go to a <scene name='60/603296/Secundaria/5'>polar view</scene>. Now let's <scene name='60/603296/Secundaria/7'>hide hydrogen atoms</scene>. The polypeptide chain backbone is coiled and placed at the center of structure, while amino acid side chains protrude outward from this backbone. Let's <scene name='60/603296/Secundaria/8'>hide side chains</scene> for a better understanding. Now, let's back to a <scene name='60/603296/Secundaria/10'>side view</scene>. A <scene name='60/603296/Secundaria/11'>ribbon model</scene> highlights the helical folding of the backbone. Using again a <scene name='60/603296/Secundaria/12'>ball and stick model</scene> we recover <scene name='60/603296/Secundaria/13'>side chains</scene>, now highlighted with a spectral color series. ''Alpha helix'' structure becomes stabilized by many <scene name='60/603296/Secundaria/14'>hydrogen bonds</scene>. All peptide groups in the chain are involved in these hydrogen bonds. <scene name='60/603296/Secundaria/15'>Zoom in</scene> to a better understanding.
:*Primary structure specifies secondary structure, i.e., is the amino acid sequence which determines that a polypeptide chain folds resulting in an alpha helix or other secondary structure. Let's consider the effects of <scene name='60/603296/Secundaria/20'>electrical charged residues</scene> of either sign and the <scene name='60/603296/Secundaria/21'>side chains size</scene>.
:*'''<scene name='60/603296/Secundaria2/1'>Beta sheet</scene>'''.- Polypeptide chain is folded in zigzag arrangement. Let's <scene name='60/603296/Secundaria2/2'>hide hydrogen atoms</scene> and <scene name='60/603296/Secundaria2/3'>side chains</scene> for a better understanding. Notice that a polypeptide chain can have several linear fragments separated by curvatures called ''beta turns''. Now let's recover <scene name='60/603296/Secundaria2/4'>side chains</scene> and highlight the <scene name='60/603296/Secundaria2/5'>hydrogen bonds</scene> between different linear sections of the chain. This hydrogen bonds give stability to the structure. Let's look now the polypeptide chain represented by a <scene name='60/603296/Secundaria2/6'>ribbon model</scene>.

== Files for 3D printer ==
 An protein alpha helix in different representations by [[User:Marius Mihasan|Marius Mihasan]] [https://3dprint.nih.gov/discover/3dpx-014891 ]
</StructureSection>
== References ==
<references/>
[[Category:3D printer files]]

Proteins: primary and secondary structure

2021-12-08T18:34:09Z

Meghan Wright: changed "alfa helix" to "alpha helix"

[[es:Proteins: primary and secondary structure (Spanish)]]
[[hi:Proteins: primary and secondary structure (Hindi)]]

<StructureSection load='' size='500' side='right' caption='' scene='60/603296/Primaria/2'>
<big>
*'''Primary structure'''
:*In this <scene name='60/603296/Primaria/2'>initial view</scene> we can see a short fragment of a polypeptide chain in order to analyze some features of its ''primary structure''. Atoms forming the chain ''backbone'' are disposed in zig-zag, as required by geometry of its bonding orbitals. Side chains of amino acid residues (or R groups) protrude outwards either side of backbone.
:*Let's go now to a <scene name='60/603296/Primaria3/1'>peptide bond</scene> between two amino acid residues. Because phenomenon of resonance, peptide bond shows some features of a double bond, which prevents free rotation of atoms on either bond side. So, six atoms marked in <scene name='60/603296/Primaria3/7'>rectangle</scene> on model window are always confined to the same rigid flat. We can test it by <scene name='60/603296/Primaria3/6'>activate rotation</scene>.
:*Polypeptide chain backbone consist in a monotonous succession in wich the following sequenze repeats: <scene name='60/603296/Primaria3/8'>alfa carbon</scene>, <scene name='60/603296/Primaria3/9'>carboxyl group carbon</scene>, <scene name='60/603296/Primaria3/11'>amino group nitrogen</scene>. Minding the restrictions to free rotation in ''peptide bond'', we can visualize the polypeptide chain as a succession of <scene name='60/603296/Primaria3/12'>rigid flats</scene>. Each of these rigid flats can freely rotate respect each other.

*'''Secondary structure'''.- In most proteins there are two main types of secondary structure.
:*<scene name='60/603296/Secundaria/4'>Alpha helix</scene>.- It is a helical structure with a thread pitch of 0.56 nm. Let's go to a <scene name='60/603296/Secundaria/5'>polar view</scene>. Now let's <scene name='60/603296/Secundaria/7'>hide hydrogen atoms</scene>. The polypeptide chain backbone is coiled and placed at the center of structure, while amino acid side chains protrude outward from this backbone. Let's <scene name='60/603296/Secundaria/8'>hide side chains</scene> for a better understanding. Now, let's back to a <scene name='60/603296/Secundaria/10'>side view</scene>. A <scene name='60/603296/Secundaria/11'>ribbon model</scene> highlights the helical folding of the backbone. Using again a <scene name='60/603296/Secundaria/12'>ball and stick model</scene> we recover <scene name='60/603296/Secundaria/13'>side chains</scene>, now highlighted with a spectral color series. ''Alfa helix'' structure becomes stabilized by many <scene name='60/603296/Secundaria/14'>hydrogen bonds</scene>. All peptide groups in the chain are involved in these hydrogen bonds. <scene name='60/603296/Secundaria/15'>Zoom in</scene> to a better understanding.
:*Primary structure specifies secondary structure, i.e., is the amino acid sequence which determines that a polypeptide chain folds resulting a alfa helix or other secondary structure. Let's consider the effects of <scene name='60/603296/Secundaria/20'>electrical charged residues</scene> of either sign and the <scene name='60/603296/Secundaria/21'>side chains size</scene>.
:*'''<scene name='60/603296/Secundaria2/1'>Beta sheet</scene>'''.- Polypeptide chain is folded in zigzag arrangement. Let's <scene name='60/603296/Secundaria2/2'>hide hydrogen atoms</scene> and <scene name='60/603296/Secundaria2/3'>side chains</scene> for a better understanding. Notice that a polypeptide chain can have several linear fragments separated by curvatures called ''beta turns''. Now let's recover <scene name='60/603296/Secundaria2/4'>side chains</scene> and highlight the <scene name='60/603296/Secundaria2/5'>hydrogen bonds</scene> between different linear sections of the chain. This hydrogen bonds give stability to the structure. Let's look now the polypeptide chain represented by a <scene name='60/603296/Secundaria2/6'>ribbon model</scene>.

== Files for 3D printer ==
 An protein alpha helix in different representations by [[User:Marius Mihasan|Marius Mihasan]] [https://3dprint.nih.gov/discover/3dpx-014891 ]
</StructureSection>
== References ==
<references/>
[[Category:3D printer files]]