How are the amino acids linked together ? which is?
By peptide links . Amide functional group
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What is the primary structure of proteins
Sequence of the 20 different naturally occurring amino acids joined together by condensation reactions with peptide links
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peptide link
C(o)-NH
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What is an alpha helix
3D arrangement of AAs with the polypeptide chain in a corkscrew shape held in place by H bonds between the H of N-H group and the O of the C=O of the 4th AA along in the chain
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Where are the R groups on the amino acid all pointed to?
The outside of the helix
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What can the secondary structure also take the form of
B pleated sheet
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How do protein chains fold
Into parallel strands side by side
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How is the protein chain held into a pleated shape ?
Hydrogen bonds between the H of the NH group and the O of the C=O of the amino acid much further along the chain in the parallel region
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What is the tertiary structure ?
Folding of the secondary structure into more complex shapes
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How is it held in place
By interactions between the R side groups in more distant AAs
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What can these be
A variety of interaction
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Including
Hydrogen bonding, sulfur-sulfur bonds and ionic interactions
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Where can H bonds form
B/w two serine side chains in diff parts of the folded chain (other AAs chains can also H bond)
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How could Ionic interactions form
Between acidic Amino acids such as aspartic acid and basic AA such as lysine
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How
There is a transfer of H ion from the -COOH to the -NH2 group to form zwitterions just as in simple AA
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How is a sulfur bridge, which is a covalent bond formed
When 2 cysteine side chains end up near each other due to folding in the protein chain, they can react to form a sulfur bridge
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What is the active site of an enzyme ?
Usually a hollow in the globular protein structure into which a substrate molecule can bond to the AA side chains through a variety of interactions
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What are the variety of interactions
Hydrogen bonding, Van der Waals forces, Permanent dipole forces, Ionic interactions
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What do the interactions need to be
Strong enough to hold the substrate for long enough for the enzyme catalysed reaction to occur but weak enough for the product to be released
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What will fit and bind to the AS
Only substrate molecules with the right shape and correct position of functional groups will
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What is this called
Lock and Key hypothesis
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What is it called when the enzyme bonds to the AS
enzyme- substrate complex
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What is the substrate is chiral
Likely the only one enantiomer will fit in the enzyme and so only one isomer will be catalysed
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eg
Strong binding and weak binding
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What do many drugs act as
Enzyme inhibitors by blocking the active site
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What will the inhibitor often bind to
The AS strongly so stopping the substrate attaching to the enzyme
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What can some inhibitors also do
Attach elsewhere on the enzyme but in doing so can change the shape of the AS which also stops its effectiveness
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What can computers be used to help
Design such drugs
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Card 2
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How are the amino acids linked together ? which is?
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