This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

Proteins: primary and secondary structure

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 18:36, 21 March 2016

Primary structure

In this 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 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 on model window are always confined to the same rigid flat. We can test it by .
Polypeptide chain backbone consist in a monotonous succession in wich the following sequenze repeats: , , . Minding the restrictions to free rotation in peptide bond, we can visualize the polypeptide chain as a succession of . Each of these rigid flats can freely rotate respect each other.

Secondary structure.- In most proteins are two main types of secondary structure.

.- It is a helical structure with a thread pitch of 0.56 nm. Let's go to a . Now let's . 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 for a better understanding. Now, let's back to a . A highlights the helical folding of the backbone. Using again a we recover , now highlighted with a spectral color series. Alfa helix structure becomes stabilized by many . All peptide groups in the chain are involved in these hydrogen bonds. 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 of either sign and the .
.- Polypeptide chain is folded in zigzag arrangement. Let's and for a better understanding. Notice that a polypeptide chain can have several linear fragments separated by curvatures called beta turns. Now let's recover and highlight the 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 .

References

Proteopedia Page Contributors and Editors (what is this?)

Alejandro Porto, Dinesh Kulhary, Eric Martz, Joel L. Sussman, Meghan Wright, Jaime Prilusky

Retrieved from "http://52.214.119.220/wiki/index.php/Proteins:_primary_and_secondary_structure"

@@ Line 8: / Line 8: @@
 *'''Secondary structure'''.- In most proteins are two main types of secondary structure.
 :*<scene name='60/603296/Secundaria/4'>Alfa 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 chais size</scene>.
+:*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>'''.- La cadena polipeptídica adopta una disposición en zig-zag, que apreciaremos mejor si <scene name='60/603296/Secundaria2/2'>ocultamos los hidrógenos</scene> y si hacemos lo propio con <scene name='60/603296/Secundaria2/3'>las cadenas laterales</scene>. Obsérvese que una misma cadena polipeptídica puede presentar tramos rectilíneos con estructura secundaria en ''lámina beta'' separados por curvaturas con estructura en ''codo beta''. A continuación vamos a restituir las <scene name='60/603296/Secundaria2/4'>cadenas laterales</scene> a su lugar y a visualizar los <scene name='60/603296/Secundaria2/5'>puentes de hidrógeno</scene> entre distintos tramos de la cadena que estabilizan la estructura. Por último veamos la misma cadena polipeptídica representada mediante un <scene name='60/603296/Secundaria2/6'>modelo de cintas</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>.
 </StructureSection>
 == References ==
 <references/>

Proteins: primary and secondary structure

From Proteopedia

Revision as of 18:36, 21 March 2016

References

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox