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Protein Modeling C

Posted: October 22nd, 2014, 6:52 pm
by fantasyfan
I'm surprised nobody's started this one up yet, but here goes nothing...
Today's question comes to you in three parts:

Name the two amino acids that contain sulfur and their one and three letter abbreviations,

Identify which one forms a disulfide bond

Explain why the other aa can't form such a bond

Re: Protein Modeling C

Posted: October 22nd, 2014, 7:10 pm
by bernard
Cysteine (Cys, C) and Methionine (Met, M) both contain sulfur. Cysteine forms disulfide bonds. Methionine cannot form disulfide bonds because the sulfur it contains is connected to a methyl group.

Re: Protein Modeling C

Posted: October 22nd, 2014, 7:15 pm
by fantasyfan
bernard wrote:
Cysteine (Cys, C) and Methionine (Met, M) both contain sulfur. Cysteine forms disulfide bonds. Methionine cannot form disulfide bonds because the sulfur it contains is connected to a methyl group.
Exactly correct, your turn!

Re: Protein Modeling C

Posted: October 22nd, 2014, 8:48 pm
by bernard
Briefly describe primary, secondary, tertiary, and quaternary structure of proteins. What level of structure does the following protein have? Describe where you see each level of structure present and how you know certain levels do not apply to this protein.

Re: Protein Modeling C

Posted: October 22nd, 2014, 9:34 pm
by fantasyfan
bernard wrote:Briefly describe primary, secondary, tertiary, and quaternary structure of proteins. What level of structure does the following protein have? Describe where you see each level of structure present and how you know certain levels do not apply to this protein.
Primary Structure is the order of amino acids in a protein

Secondary Structure has to do with the orientation of the protein backbone subunits relative to each other and where the hydrogen bonds form. Results primarily in alpha-helices and beta-pleated sheets

Tertiary Structure is the overall shape of a protein which results from a combination of many factors. It determines the function of the protein

Quaternary structure involves multiple individual chains of protein interacting to form one larger protein, such as in the four subunits of hemoglobin

This protein has primary, secondary, and tertiary structure. All proteins must have these three structures. Primary is the order of the subunits, and thus in having subunits the protein has a primary structure. The secondary structure is visible in the coils (helices) and parallel folded lines (pleated sheets). Tertiary structure is evident in the position of all of these structures relative to each other. There is no quaternary structure in this protein because there is only one chain present.

Re: Protein Modeling C

Posted: October 22nd, 2014, 10:35 pm
by bernard
fantasyfan wrote:
bernard wrote:Briefly describe primary, secondary, tertiary, and quaternary structure of proteins. What level of structure does the following protein have? Describe where you see each level of structure present and how you know certain levels do not apply to this protein.
Primary Structure is the order of amino acids in a protein

Secondary Structure has to do with the orientation of the protein backbone subunits relative to each other and where the hydrogen bonds form. Results primarily in alpha-helices and beta-pleated sheets

Tertiary Structure is the overall shape of a protein which results from a combination of many factors. It determines the function of the protein

Quaternary structure involves multiple individual chains of protein interacting to form one larger protein, such as in the four subunits of hemoglobin

This protein has primary, secondary, and tertiary structure. All proteins must have these three structures. Primary is the order of the subunits, and thus in having subunits the protein has a primary structure. The secondary structure is visible in the coils (helices) and parallel folded lines (pleated sheets). Tertiary structure is evident in the position of all of these structures relative to each other. There is no quaternary structure in this protein because there is only one chain present.
Very good! Your turn.

Re: Protein Modeling C

Posted: October 23rd, 2014, 10:08 am
by fantasyfan
What is the function or the CCR5 protein, and how does the Δ32 mutation help prevent HIV infection of a cell?

Re: Protein Modeling C

Posted: October 27th, 2014, 2:11 pm
by Gemma W
fantasyfan wrote:What is the function or the CCR5 protein, and how does the Δ32 mutation help prevent HIV infection of a cell?
The CCR5 protein is a chemokine receptor on the human T helper cells. In relation to this year's event, it is one of the co-receptors that binds to the HIV virus, allowing it to pierce the cell membrane and enter the cell. The Δ32 mutation prevents HIV infection by rendering the CCR5 protein nonfunctional, thereby preventing it from binding to the HIV. People without CCR5 protein or with reduced levels of the protein are otherwise healthy, but have T cells that are resistant to HIV. Yay!

Re: Protein Modeling C

Posted: October 27th, 2014, 2:29 pm
by fantasyfan
Gemma W wrote:Yay!
That's correct, your turn

Re: Protein Modeling C

Posted: November 2nd, 2014, 1:33 pm
by Gemma W
What Jmol command would one use to display only this year's section of the fokI protein? (Chain A, residues 421 to 560)