Gene Structure and Domain Determination Quiz

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What can start codons, TATA boxes, and polyA addition sites determine?

UTRs

Exons (correct)

Codon biases

Introns

What is a common indicator of transmembrane segments in proteins?

Polar side chains

Short alpha helices

Aromatic residues at the ends of helices (correct)

Loose packing of helices

What can the presence of S-S bonds or metal ions indicate about a protein domain?

The domain is highly polar

The domain is stabilized (correct)

The domain has introns

The domain is hydrophobic

Which feature is typical of low complexity segments in protein sequences?

Presence of overlapping repeats Signup and view all the answers

What does the dotplot method help detect in protein sequences?

Transmembrane segments Signup and view all the answers

Why can topography and the presence of multiple segments be challenging for predicting transmembrane proteins?

They complicate the identification of segment boundaries Signup and view all the answers

What is an indicator that an alpha-helix has been broken?

Proline is an alpha-helix breaker Signup and view all the answers

What is one issue with loops?

Disorganized, hard to predict because they are less conserved, may not interact with other proteins Signup and view all the answers

How do we predict secondary structures?

Alpha Fold (neural network method) Signup and view all the answers

What does Ramachandran plot do?

Determines possible torsion angles that are energetically favorable Signup and view all the answers

How are force fields created?

Energy levels used to create a force field of possible rotations. Lowest energy state is native structure typically Signup and view all the answers

What can force fields do?

Calculate the potential energy of a conformational state which may include molecules such as solvents Signup and view all the answers

Gene Structure and Domain Determination Quiz

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Questions and Answers

What can start codons, TATA boxes, and polyA addition sites determine?

What is a common indicator of transmembrane segments in proteins?

What can the presence of S-S bonds or metal ions indicate about a protein domain?

Which feature is typical of low complexity segments in protein sequences?

What does the dotplot method help detect in protein sequences?

Why can topography and the presence of multiple segments be challenging for predicting transmembrane proteins?

What is an indicator that an alpha-helix has been broken?

What is one issue with loops?

How do we predict secondary structures?

What does Ramachandran plot do?

How are force fields created?

What can force fields do?

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