Protein Structure and Amino Acid Sequence

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What is the primary determinant of protein structure?

Peptide backbone

Amino acid sequence (correct)

Hydrogen bonds

Hydrophobic interactions

What type of interactions are the major contributors to protein structure stabilization?

Electrostatic interactions

Van der Waals interactions

Hydrophobic interactions (correct)

Covalent bonds

What determines the local folding patterns of the polypeptide chain?

Amino acid sequence

Peptide bond formation

Hydrogen bonds between adjacent residues

Phi and psi angles of the peptide backbone (correct)

In an alpha helix, what is the typical spacing of hydrogen bonds between residues?

Four residues Signup and view all the answers

What type of structures are stabilized by hydrogen bonds between adjacent strands of the polypeptide chain?

Beta sheets Signup and view all the answers

What is the function of hydrogen bonds in protein secondary structures?

To stabilize specific conformations Signup and view all the answers

What is the direction of H-bonded strands in antiparallel β sheets?

Opposite directions Signup and view all the answers

What is the primary function of a β turn?

To connect two adjacent β sheets Signup and view all the answers

What is typically plotted on the x-axis of a Ramachandran plot?

φ angles Signup and view all the answers

What is a common feature of protein motifs?

A specific function or structure Signup and view all the answers

What is the typical number of amino acids involved in a β turn?

4 Signup and view all the answers

What is the purpose of a Ramachandran plot in protein structure analysis?

To validate and determine protein structure Signup and view all the answers

What is a major challenge in using X-ray crystallography to determine protein structures?

Producing high-quality protein crystals Signup and view all the answers

What is the primary application of Coot in structural biology?

Model building and visualization Signup and view all the answers

What is the phenomenon exploited by NMR spectroscopy?

Nuclear magnetic resonance Signup and view all the answers

Why is X-ray crystallography often preferred over NMR spectroscopy?

It provides higher-resolution structural data Signup and view all the answers

What is the typical precision of atomic positions in X-ray crystallography?

Sub-angstrom Signup and view all the answers

What type of molecules can be analyzed using NMR spectroscopy?

Small organic molecules, peptides, and proteins Signup and view all the answers

What is the typical precision range for atom positions determined using NMR spectroscopy?

1-3 angstroms Signup and view all the answers

What is the purpose of flash-freezing samples in Cryo-EM?

To visualize molecules in their native environment Signup and view all the answers

What is the primary function of CryoSPARC software?

To process cryoEM images and perform 3D reconstruction Signup and view all the answers

Which software package is widely used for cryoEM image processing and 3D reconstruction?

RELION Signup and view all the answers

What is the basis for identifying and characterizing molecules using Mass Spectrometry?

Mass-to-charge ratio Signup and view all the answers

In which fields is Mass Spectrometry widely used?

Chemistry, environmental science, proteomics, and metabolomics Signup and view all the answers

What is the purpose of mass spectrometry in proteomics?

To identify and characterize proteins and their modifications Signup and view all the answers

What is the difference between bottom-up and top-down proteomics?

Bottom-up involves digestion of proteins into peptides, while top-down involves intact proteins Signup and view all the answers

What is the purpose of protein databases in proteomics?

To store information about protein structures and functions Signup and view all the answers