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My report on "Four Levels of Protein Structure"
My report on "Four Levels of Protein Structure"
Student name: Giulia Baldon
Teacher name: Perroteau
School: university of Torino
Submission Time: 07/10/09 16.28
Page 1 : http://mw2.concord.org/public/part2/proteinfolding/page1.cml
1. A protein that can puncture a cell wall:
(a) protein 1
(b) protein 2
(c) protein 3
My answer is (b) (14.09.26)
2. A protein that forms a cable:
(a) protein 1
(b) protein 2
(c) protein 3
My answer is (a) (14.09.33)
3. A protein that becomes a pore in a membrane:
(a) protein 1
(b) protein 2
(c) protein 3
My answer is (c) (14.09.35)
Page 2 : http://mw2.concord.org/public/part2/proteinfolding/page2.cml
1. Put a snapshot of the surface of the protein here.
(14.16.41)
2. Create an image that clearly shows both ends of the string of amino acids. In the snapshot, use the text annotation tool to mark both ends.
(14.17.50)
Page 3 : http://mw2.concord.org/public/part2/proteinfolding/page3.cml
1.
(14.15.09)
2. Use the link above to open and explore the 20 rotatable 3D amino acids. Then select the "Sidechain" color scheme. The atoms that are colored gray are the same in every amino acid. What are they called?
(a) the sidechain atoms
(b) the backbone atoms
(c) the protein atoms
My answer is (b) (14.15.36)
3. On the page of 3D amino acids, find glutamine and histidine. Use the different color schemes to select the true statement(s) below. (More than one statement may be true).
(a) they are both polar amino acids
(b) one is polar and the other is non-polar
(c) one of them is charged
(d) they are both non-polar
My answer is (a) (c) (14.16.11)
Page 4 : http://mw2.concord.org/public/part2/proteinfolding/page4.cml
1. Describe the distribution of electrons and polarity of an O-H bond.
Nel legame O-H, a causa della forte elettronegatività dell'ossigeno, si crea una molecola polare con polo negativo in prossimità dell'O (che attira gli elettroni dell'H), e polo positivo in corrispondenza dell'H. (14.12.41)
2. Describe the distribution of electrons and polarity of a C-H bond.
Il legame C-H è debolmente polare, con polo negativo in corrispondenza di C e polo positivo in corrispondenza di H. (14.13.28)
Page 5 : http://mw2.concord.org/public/part2/proteinfolding/page5.cml
1. Snapshot of asparagine:
Polare (14.22.50)
2. Snapshot of leucine:
Non polare (14.22.58)
3. Snapshot of threonine:
Polare (14.23.04)
4. For Asparagine, which surface shows the correct charges?
(a) surface 1
(b) surface 2
My answer is (a) (13.07.00)
5. Which surface shows the correct charges for Leucine?
(a) surface 3
(b) surface 4
My answer is (b) (13.07.27)
6. Which surface shows the correct charges for Threonine?
(a) surface 5
(b) surface 6
My answer is (a) (13.07.40)
7. Choose the best way to complete this sentence: When two atoms in a bond have very different electronegativities, the surface of the molecule...
(a) has no charge.
(b) has regions of positive and negative charge.
(c) has a negative charge.
(d) has a positive charge.
My answer is (b) (13.08.01)
8. Explain how the colors on the surfaces of the side chains indicate whether it is polar or non-polar.
Se il legame è polare, la superficie presenta una colorazione blu in prossimità del polo negativo della molecola e una colorazione rossa in corrispondenza del polo positivo. Se invece il legame non è polare, la superficie della molecola non viene colorata. (13.09.39)
Page 6 : http://mw2.concord.org/public/part2/proteinfolding/page6.cml
1. Is water a polar or non-polar molecule? Explain your answer by writing about the bonds in water.
La molecola d'acqua è polare a causa della forte attrazione del nucleo dell'ossigeno per gli elettroni. Perciò la regione che circonda ogni nucleo di idrogeno è debolmente positiva. (14.02.42)
2. Which type of amino acid is hydrophobic?
(a) polar
(b) non-polar
(c) neither - they both don't attract water very well
(d) neither - they attract the water molecules equally
My answer is (b) (14.03.36)
3. Use your knowledge of positive and negative charge to explain why polar molecules attract each other and water better than non-polar molecules.
La molecola d'acqua, presentando un polo positivo e un polo negativo, attira altre molecole polari: il polo negativo dell'acqua verrà attirato da quello positivo della molecola polare e viceversa. In presenza di una molecola non polare invece non si presenta questo tipo di attrazione. (14.06.13)
4. Which solvent(s) leads to folding of the protein?
(a) both water and oil
(b) neither water nor oil
(c) water
(d) oil
My answer is (c) (14.07.01)
5. Where do the amino acids with polar side chains end up when the protein chain folds?
(a) evenly throughout the folded protein
(b) mostly inside the folded protein
(c) mostly on the outside of the folded protein
My answer is (c) (14.07.46)
Page 7 : http://mw2.concord.org/public/part2/proteinfolding/page7.cml
Page 8 : http://mw2.concord.org/public/part2/proteinfolding/page8.cml
1. Snapshot of an alpha helix:
(14.32.29)
2. Snapshot of a beta sheet:
(14.35.03)
3. A loop between a beta sheet and an alpha helix:
(14.37.02)
Page 9 : http://mw2.concord.org/public/part2/proteinfolding/page9.cml
1. The hydrogen bonds that stabilize an alpha helix.
(14.42.47)
2. The hydrogen bonds that stabilize a beta sheet.
(14.43.13)
3. Hydrogen bonds stabilizing alpha helices and beta sheets form between the atoms of which part(s) of the amino acids involved?
(a) the side chains
(b) the side chains and backbone
(c) the backbone
My answer is (c) (14.43.39)
4. Place a snapshot here that illustrates your answer to the previous question.
I legami ad idrogeno stabilizzano la struttura secondaria (14.50.15)
Page 10 : http://mw2.concord.org/public/part2/proteinfolding/page10.cml
1. Show an interaction that stabilizes an alpha helix and a loop:
Salt bridges (14.56.39)
2. Show an interaction that stabilizes two alpha helices:
Hydrogen bonds (15.02.29)
3. Show an interaction that stabilizes a loop and a beta sheet:
Salt bridges (15.00.12)
4. Show the hydrophobic core:
(15.00.41)
Page 11 : http://mw2.concord.org/public/part2/proteinfolding/page11.cml
1. On the left is a different small molecule than NAD. Why wouldn't this molecule bind to alcohol dehydrogenase in place of NAD? (Choose the BEST answer below).
(a) it is not the same as NAD
(b) it is smaller than NAD
(c) it is too large to fit in the NAD site
(d) it's the wrong shape, and will not form attractions with the site
My answer is (d) (15.08.09)
2. What would you expect to happen to the function of proteins at very high temperatures?
(a) the functions would not be affected
(b) the proteins would not be able to function anymore
(c) the functions would happen faster
My answer is (b) (15.10.39)
3. Explain how protein folding fits in to your answer to the previous question.
Con l'aumento della temperatura, si determina anche un aumento dell'energia delle molecole (cinetica). L'aumento di temperatura fa sì che le molecole non riescano a mantenere la forma originaria, compromettendo pertanto la funzionalità della proteina. (15.13.54)
Page 12 : http://mw2.concord.org/public/part2/proteinfolding/page12.cml
1. Does TNF have the quaternary level of structure? Make sure to try different color schemes on the model of TNF above.
(a) yes
(b) no
(c) it's impossible to tell.
My answer is (a) (15.18.17)
2. Explain your answer to the previous question:
La TNF ha una struttura quaternaria poichè è formata da 3 subunità collegate fra loro che funzionano come una sola unità.Inoltre è classificale come omotrimero poichè le subunità sono 3 e sono identiche tra loro. (15.22.29)
Page 13 : http://mw2.concord.org/public/part2/proteinfolding/page13.cml
1. The "primary structure" of a protein refers to:
(a) the folds of the protein
(b) the alpha helix and beta sheet structures
(c) the sequence of amino acids in the protein
(d) two proteins that function as a unit
My answer is (c) (15.22.47)
2. What part of an amino acid has properties (shape, charge) that are different from other amino acids?
(a) the side chain
(b) the backbone atoms
(c) the secondary structure
(d) none of the above
My answer is (d) (15.27.05)
3. The bond between two atoms of equal electronegativity is:
(a) polar
(b) hydrophilic
(c) nonpolar
My answer is (c) (15.23.38)
4. The protein shown at right has folded in water. Which of the following statements about it is FALSE?
(a) amino acid 14 is most likely hydrophobic
(b) amino acid 17 is most likely polar
(c) amino acid 22 is most likely polar
(d) amino acid 20 is most likely hydrophilic
My answer is (c) (15.24.17)
5. Which of the following do hydrogen bonds help to stabilize?
(a) primary structure
(b) secondary structure
(c) tertiary structure
(d) quaternary structure
(e) B, C, and D are correct
My answer is (e) (16.16.01)
6. Select two correct choices: A protein with quaternary structure...
(a) is made of two or more strings of amino acids
(b) is always composed of identical subunits
(c) is always composed of different subunits
(d) can be a mix of identical and different subunits
My answer is (a) (d) (15.25.09)
7. Two amino acids that are far apart from each other in the primary structure of a protein can be touching each other in the tertiary structure of the same protein. Explain how this happens.
Due amminoacidi che nella struttura primaria erano distanti fra loro possono trovarsi vicini nella struttura terziaria della medesima proteina poichè la struttura terziaria è il risultato di interazioni tra i gruppi R degli amminoacidi che la compongono( interazioni idrofobiche, attrazione tra sequenze di carica opposta, legami covalenti, legami idrogeno). (16.26.33)
8. Why do defects in protein folding cause disease?
Perchè la funzionalità di una proteina è strettamente collegata alla sua forma. Difetti nella forma provocano ne impediscono il corretto funzionamento. (16.28.04)
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8.0
8.0
128 128 1288
8.0
8.0
8.0
8.0
truetrue13
8.0
8.0
truetrue13
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
128 128 1288
8.0
8.0
8.0
8.0
truetrue13
8.0
8.0
truetrue13
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0
128 128 1288
8.0
8.0
8.0
8.0
truetrue13
8.0
8.0
truetrue13
8.0
8.0
128 128 1288
8.0
8.0
8.0
8.0
truetrue13
8.0
8.0
truetrue13
8.0
8.0
128 128 1288
8.0
8.0
8.0
8.0
8.0
8.0
8.0
8.0