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48 Cards in this Set
- Front
- Back
Why is there no free rotation around the amide plane? |
Due to delocalisation of electrons |
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What bonds can rotate in a protein? |
All bonds except the peptide bonds (phi and psi bonds) |
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What stabilises the alpha helix? |
H bonds between C=O and N-H |
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Roughly what length is a hydrogen bond? |
0.28 nm |
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What is the enthalpy of a hydrogen bond and why is this termed weak? |
3 kcal/mol H bond weak when compared to covalent bond |
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What are structural proteins build from? |
Alpha helices |
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Why does a beta sheet have to be anti-parallel? |
So hydrogen bonds are at right angles to the strands |
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What are some features of the beta sheet? |
Very flexible but immensely strong because of H bonds |
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What happens if chains run in the same direction? |
H bonds are not aligned |
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What are the two key points to remember about beta sheets? |
1. They are a secondary structural feature 2. They are stabilised by H bonds between strands |
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What is the difference between the two types of B-turn? |
Carbonyls point in different directions |
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Why is this a disallowed conformation? |
N-H and O would crash into each other |
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What is the Ramachandran plot? |
Only certain combinations of phi and psi angles values are found in proteins, presumably because of steric hinderances hat prevent other combinations. In the plot, phi and psi angles adopted by each amino acid in a large number of proteins are plotted against each other. They clearly form two tight clusters, which correspond to the angles found in the alpha helices and beta pleated sheets. |
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What is special about the highlighted regions in the Ramachandran plot? |
There is no steric clashing |
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What is the structure like of collagen? |
It is a triple helix made up of left handed helices but the super helix ( 3 strands) is right handed. |
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Is an alpha helix a single chain or made of multiple chains? |
A single chain |
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What kind of proteins does the alpha helix form? |
Globular and fibrous proteins ( e.g keratin) |
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Where are hydrogen bonds found in an alpha helix? |
Within the chain |
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How many residues are there per turn in an alpha helix? |
3.6 |
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Is the alpha helix right or left handed? |
Right |
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Is the alpha super helix right or left handed? |
Left |
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Which amino acid is not found in an alpha helix and why? |
Proline It will break the chain |
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Where are hydrogen bonds found in collagen? |
Between chains |
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How many residues per turn are there in collagen? |
3 |
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Why is every third amino acid in collagen glycine? What are the other amino acids? (Gly-X-Y) |
It is the smallest amino acid that can fit into spaces that other amino acids could not X= mainly proline Y = mainly hydroxy proline |
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How many strands of beta sheets are needed to form a beta barrel? |
8 |
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What does the beta barrel enclose? |
Tightly packed hydrophobic side chains |
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In a protein, how are the alpha helix and B pleated sheet section connected? |
By an unstructured polypeptides known as connecting loops |
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What are the two main types of super secondary structure? |
Beta barrel Alpha helix bundle |
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Some proteins consist of 2 or more domains linked together e.g pyruvate kinase. What are the 3 domains or pyruvate kinase? |
1.B-barrel 2. B sandwich 3. Rossman fold |
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As more structures are determined, it appears that there is a limited number of protein folds. What number could this be? |
200-300 |
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What is the only covalent bond that stabilises the tertiary structure of a protein? |
A disulphide bone (not all proteins contain disulphide bonds) |
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What are the non covalent forces that stabilise the folded protein structure? |
1. Hydrogen bonds 2. Electrostatic interactions ( + and - amino acids) 3. Van der Waals forces 4. Hydrophobic effect |
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What is the driving force for protein folding in water? |
Hydrophobic/hydrophilic nature of amino acids. |
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What are the two ways that a polypeptide chain can cross a membrane? |
As part of a barrel As an alpha helix |
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In the structure of haemoglobin and other globular proteins, proline is often found where the polypeptide turns a corner. Explain this. |
The structure of proline means it cannot participate in hydrogen bonding in the alpha helix or beta pleated sheet, but its shape fits perfectly into a "reverse" turn (beta turn) |
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Why do histone proteins, which bind DNA, contain a high proportion of lysine and arginine residues? |
Lysine and arginine have basic (positively charged) side chains, which can interact with acidic (negatively charged) DNA. |
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What is the pitch of an alpha helix? |
The length of one complete turn |
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How long is the pitch of an alpha helix? |
0.54 nm |
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How many residues are there per turn in an alpha helix? |
3.6 |
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What is a Rossman fold? |
beta alpha beta |
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There is a limited number of protein folds, so what are many proteins made up of? |
Several commonly occurring domains or “modules” |
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How is the alpha helix stabilised? |
By hydrogen bond formation between the oxygen atom attached to thecarbon atom of one peptide bond and that of the hydrogen atom attached to the nitrogenatom of the fourth peptide bond (inclusive) along the chain. |
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Where are the R-groups of the residues in the -helical conformation |
They point away from the axis |
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What kind of conformation is a connecting loop in? |
Any conformation (other than a recognisable alpha helix or beta pleated sheet) |
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What is the beta barrel? |
A central core of beta strands that are twisted. The barrel enclose tightly packed hydrophobic side chains. |
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What determines the folded structure of a protein? |
The amino acid sequence of the polypeptide chain. |
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What is the tertiary structure of a protein? |
The arrangement of the various secondary structures into the compact structure of a globular protein. |
