Tutorial:How do we get the oxygen we breathe: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| (13 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
{{BAMBED | |||
|DATE=August 2, 2012 | |||
|OLDID=1512482 | |||
|BAMBEDDOI=10.1002/bmb.20646 | |||
}} | |||
__NOTOC__ | __NOTOC__ | ||
<StructureSection load='1hh0' size='500' side='right' caption='' scene=' | <StructureSection load='1hh0' size='500' side='right' caption='' scene='Hemoglobin/Foursubunits/5' > | ||
<div style='background-color:yellow;padding:10px;margin:10px;'>This tutorial is designed for high school and beginning college students (ages 14-19). A more detailed tutorial is available at [[Hemoglobin]]</div> | |||
When we breathe, or respire, oxygen from the air is taken up by blood in our lungs and soon delivered to each of the cells in our body through our circulatory system. Among other uses, our cells use oxygen as the final electron acceptor in a process called aerobic respiration -- a process that converts the energy in food and nutrients into a form of energy that the cell can readily use (molecules of ATP, adenosine triphosphate). The cells of large organisms like humans use aerobic respiration because other forms of energy production are less efficient, and oxygen is plentiful. (''THINK'': Do fish use aerobic respiration?) | When we breathe, or respire, oxygen from the air is taken up by blood in our lungs and soon delivered to each of the cells in our body through our circulatory system. Among other uses, our cells use oxygen as the final electron acceptor in a process called aerobic respiration -- a process that converts the energy in food and nutrients into a form of energy that the cell can readily use (molecules of ATP, adenosine triphosphate). The cells of large organisms like humans use aerobic respiration because other forms of energy production are less efficient, and oxygen is plentiful. (''THINK'': Do fish use aerobic respiration?) | ||
| Line 11: | Line 17: | ||
=====Hemoglobin is a tetramer===== | =====Hemoglobin is a tetramer===== | ||
In the three-dimensional structure of hemoglobin to the right, you see two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_blue_chains/2'>light-blue chains</scene> and two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_green_chains/1'>light-green chains</scene>. (''Drag the hemoglobin structure with the mouse to rotate it. To zoom, use your scroll-wheel, or drag while holding shift.'') These are the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_four_monomers/1'>four monomers</scene> of the hemoglobin molecule, and they are shown in a cartoon-style representation where a single curved line connects the α-carbons in the amino acids of each chain and the [[secondary structure]] α-helices are shown as simplified cartoon helices. Because hemoglobin is composed of four monomers, it is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_tetramer/2'>tetramer</scene>. The two types of monomers that make up the hemoglobin tetramer are distinguished by their color: the two α<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_alpha_monomers/1'>-monomers</scene> in light-blue and the two β<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_beta_monomers/1'>-monomers</scene> in light-green. Each α-monomer is a chain of 141 amino acids and each β-monomer is a chain of 146 amino acids. Be careful not to get confused with the context in which we use the label "α", or "alpha": remember that both the α- and the β-monomers contain α-carbons and α-helices. (''THINK'': How many amino acids does it take to build a molecule of hemoglobin?) | In the three-dimensional structure of hemoglobin to the right, you see two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_blue_chains/2'>light-blue chains</scene> and two <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_light_green_chains/1'>light-green chains</scene>. (''Drag the hemoglobin structure with the mouse to rotate it. To zoom, use your scroll-wheel, or drag while holding shift.'') These are the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_four_monomers/1'>four monomers</scene> of the hemoglobin molecule, and they are shown in a cartoon-style representation where a single curved line connects the α-carbons in the amino acids of each chain and the [[secondary structure]] α-helices are shown as simplified cartoon helices. Because hemoglobin is composed of four monomers, it is called a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_tetramer/2'>tetramer</scene>. The two types of monomers that make up the hemoglobin tetramer are distinguished by their color: the two α<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_alpha_monomers/1'>-monomers</scene> in light-blue and the two β<scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/1hho_beta_monomers/1'>-monomers</scene> in light-green. Each α-monomer is a chain of 141 amino acids and each β-monomer is a chain of 146 amino acids. Be careful not to get confused with the context in which we use the label "α", or "alpha": remember that both the α- and the β-monomers contain α-carbons and α-helices. (''THINK'': How many amino acids does it take to build a molecule of hemoglobin?) | ||
This next view shows the <scene name='Hemoglobin/Alpha2beta2/7'>tetramer</scene> in space-fill representation, with the alpha and beta chains coloured differently. | |||
=====Each monomer has a heme group===== | =====Each monomer has a heme group===== | ||
| Line 21: | Line 28: | ||
=====Capturing oxygen===== | =====Capturing oxygen===== | ||
Hemoglobin captures oxygen and transports it through the bloodstream by binding oxygen to each of its <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>four heme groups</scene>. These <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene> are prosthetic groups; they are non-protein chemical compounds that are associated with hemoglobin and are necessary for its function. Each heme is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme_composition/1'>ring molecule made up of</scene> {{Template:ColorKey_Element_C}}arbon, {{Template:ColorKey_Element_N}}itrogen, {{Template:ColorKey_Element_O}}xygen and hydrogen, with a single <font color="#E06633">'''Fe<sup>2+</sup>'''</font> (iron) ion at its center, coordinated by the four surrounding nitrogens. Each heme is roughly <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Planar_heme/1'>planar</scene>, and is held in place within the monomer by a hydrophobic interactions and a covalent bond between the iron ion and a nitrogen atom in the side chain of what is termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Proximal_histidine/1'>proximal histidine</scene>. Another histidine, termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Distal_histidine/2'>distal histidine</scene>, helps in oxygen binding by | Hemoglobin captures oxygen and transports it through the bloodstream by binding oxygen to each of its <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Four_hemes/3'>four heme groups</scene>. These <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/One_heome/2'>heme groups</scene> are prosthetic groups; they are non-protein chemical compounds that are associated with hemoglobin and are necessary for its function. Each heme is <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme_composition/1'>ring molecule made up of</scene> {{Template:ColorKey_Element_C}}arbon, {{Template:ColorKey_Element_N}}itrogen, {{Template:ColorKey_Element_O}}xygen and hydrogen, with a single <font color="#E06633">'''Fe<sup>2+</sup>'''</font> (iron) ion at its center, coordinated by the four surrounding nitrogens. Each heme is roughly <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Planar_heme/1'>planar</scene>, and is held in place within the monomer by a hydrophobic interactions and a covalent bond between the iron ion and a nitrogen atom in the side chain of what is termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Proximal_histidine/1'>proximal histidine</scene>. Another histidine, termed the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Distal_histidine/2'>distal histidine</scene>, helps in oxygen binding by preventing oxidation of the iron atom (which would prevent oxygen from binding) and by preventing other molecules from binding. | ||
When oxygen is abundant, an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>oxygen molecule binds to the iron</scene> in the heme group. (''THINK'': Are there other changes besides the oxygen binding to the iron ion? Why might there be other changes?) We can watch oxygen binding in the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/2'>context of an entire monomer</scene> (colored in rainbow colors from the N terminus of the monomer to its C terminus) or in a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>close-up view</scene> of the heme group. | When oxygen is abundant, an <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>oxygen molecule binds to the iron</scene> in the heme group (Molecular oxygen (O<sub>2</sub>) is represented by two <font color="#E06633">'''red spheres'''</font color>). (''THINK'': Are there other changes besides the oxygen binding to the iron ion? Why might there be other changes?) We can watch oxygen binding in the <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/2'>context of an entire monomer</scene> (colored in rainbow colors from the N terminus of the monomer to its C terminus) or in a <scene name='User:Jaime_Prilusky/How_do_we_get_the_oxygen_we_breathe/Heme/1'>close-up view</scene> of the heme group. | ||
{{Template:Button Toggle Animation2}} | {{Template:Button Toggle Animation2}} | ||
| Line 37: | Line 44: | ||
</StructureSection> | </StructureSection> | ||
==See Also== | ==See Also== | ||
*[[Hemoglobin]] | *[[Hemoglobin]] | ||
| Line 52: | Line 58: | ||
==Content Contributors== | ==Content Contributors== | ||
This page includes scenes, structures and ideas from [[User:Eric_Martz|Eric Martz]], [[User:Frieda S. Reichsman|Frieda S. Reichsman]] and [[User:Angel_Herraez|Angel Herraez]]. | This page includes scenes, structures and ideas from [[User:Eric_Martz|Eric Martz]], [[User:Frieda S. Reichsman|Frieda S. Reichsman]] and [[User:Angel_Herraez|Angel Herraez]]. | ||
[[Category:Featured in BAMBED]] | |||
[[cs:Tutorial:How_do_we_get_the_oxygen_we_breathe_%28Czech%29]] | |||
[[es:Tutorial:How_do_we_get_the_oxygen_we_breathe_%28Spanish%29]] | |||
