Basics of Protein Structure
From Proteopedia
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| - | Proteins perform many important functions in living organisms, including movement, immune responses, sensing the environment, energy acquisition, and catalyzing reactions. The protein shown to the right is insulin; when insulin isn't properly synthesized or | + | Proteins perform many important functions in living organisms, including movement, immune responses, sensing the environment, energy acquisition, and catalyzing reactions. The protein shown to the right is insulin; when insulin isn't properly synthesized or recognized, diabetes occurs. |
Proteins are long [[chains]] of [[Amino Acids]], and are synthesized by the [[ribosome]], using messenger [[RNA]] as a template. There are 20 amino acids commonly found in proteins. <scene name='60/604417/Ala/2'>Amino acids</scene> contain an <scene name='60/604417/Ala_amino/1'>amino group</scene>, a central carbon atom called the <scene name='60/604417/Ala_alpha/1'>alpha carbon</scene>, and a <scene name='60/604417/Ala_cooh/1'>carboxylic acid</scene>. The 20 amino acids differ by what is attached to the central atom; is variable portion is referred to as the <scene name='60/604417/Ala_side_chain/1'>side chain</scene>. The amino acid shown is alanine; its side chain is a methyl (-CH3) group. The atoms are displayed using the [[CPK|coloring convention]] '''<font color="#808080">Carbon</font>, <span style="background-color:black;color:white;"> Hydrogen </span>, <font color="red">Oxygen</font>, <font color="#3050f8">Nitrogen</font>''': {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}. | Proteins are long [[chains]] of [[Amino Acids]], and are synthesized by the [[ribosome]], using messenger [[RNA]] as a template. There are 20 amino acids commonly found in proteins. <scene name='60/604417/Ala/2'>Amino acids</scene> contain an <scene name='60/604417/Ala_amino/1'>amino group</scene>, a central carbon atom called the <scene name='60/604417/Ala_alpha/1'>alpha carbon</scene>, and a <scene name='60/604417/Ala_cooh/1'>carboxylic acid</scene>. The 20 amino acids differ by what is attached to the central atom; is variable portion is referred to as the <scene name='60/604417/Ala_side_chain/1'>side chain</scene>. The amino acid shown is alanine; its side chain is a methyl (-CH3) group. The atoms are displayed using the [[CPK|coloring convention]] '''<font color="#808080">Carbon</font>, <span style="background-color:black;color:white;"> Hydrogen </span>, <font color="red">Oxygen</font>, <font color="#3050f8">Nitrogen</font>''': {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}. | ||
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== Levels of Protein Structure == | == Levels of Protein Structure == | ||
| - | There are [[Four levels of protein structure|four different levels of protein structure]]. The <scene name='60/604417/Ins_bead_backbone_labels/1'>primary structure</scene> is the amino acid sequence. The amino acids are connected by an amide bond, made from the amino group (NH2) of one amino acid, and the carboxylic acid (C=O) from another amino acid. The amino acids are linked in a repeating pattern. The [[Backbone representations|backbone]] of the protein is the repeating N-C-C=O pattern, with the side chains projecting out from the backbone. The end with the free -NH2 group is called the Amino or <scene name='60/604417/N_terminus/1'>N terminus</scene>, while the end with a free carboxylic acid is called the <scene name='60/604417/C_terminus/1'>C terminus</scene>. The sequence of amino acids is written and numbered from the N terminus (where protein synthesis begins) to the C terminus (where amino acids are added during protein synthesis), so for <scene name='60/604417/N_to_c/1'>the segment shown</scene>, the sequence would be Val-Asn-Gln. For more practice identifying peptide bonds between amino acids, please try [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]] and [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]. | + | There are [[Four levels of protein structure|four different levels of protein structure]]. The <scene name='60/604417/Ins_bead_backbone_labels/1'>primary structure</scene> is the amino acid sequence. The amino acids are connected by an amide bond, made from the amino group (NH2) of one amino acid, and the carboxylic acid (C=O) from another amino acid. In the process of making the bond, a water molecule is removed. The amino acids are linked in a repeating pattern. The [[Backbone representations|backbone]] of the protein is the repeating <scene name='60/604417/N_calpha_co/2'>N-C-C=O</scene> pattern, with the <scene name='60/604417/Side_chains/1'>side chains</scene> projecting out from the backbone. The end with the free -NH2 group is called the Amino or <scene name='60/604417/N_terminus/1'>N terminus</scene>, while the end with a free carboxylic acid is called the <scene name='60/604417/C_terminus/1'>C terminus</scene>. The sequence of amino acids is written and numbered from the N terminus (where protein synthesis begins) to the C terminus (where amino acids are added during protein synthesis), so for <scene name='60/604417/N_to_c/1'>the segment shown</scene>, the sequence would be Val-Asn-Gln, or VNQ, if one letter abbreviations are used for the amino acids. For more practice identifying peptide bonds between amino acids, please try [[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]] and [[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]. |
| - | The second level of structure is called secondary structure, and is the shapes (conformations) formed by short sequences of amino acids. This level of structure is stabilized by <scene name=' | + | The second level of structure is called secondary structure, and is the shapes (conformations) formed by short sequences of amino acids. This level of structure is stabilized by <scene name='60/604417/H_bonds/1'>hydrogen bonds</scene> along the backbone. Hydrogen bonds are attractions between an N, O or F and a hydrogen attached to an N, O or F (More about [[hydrogen bonds]].) The two most common shapes are [[Helices in Proteins|alpha helices]] and [[Sheets in Proteins|beta strands]]. These are favored simply because [[Tutorial:Ramachandran principle and phi psi angles|two atoms cannot occupy the same space]] (steric collisions). |
==Protein Structure Data== | ==Protein Structure Data== | ||
Revision as of 03:59, 3 February 2020
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