Biology Questions: Ribosome and Protein Structure
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Questions and Answers

Can natural proteins crystallize in the crystal class -4?

  • Never
  • Yes, it is a popular class
  • Yes, but only when the crystals are twinned
  • Yes, but only in very rare cases (correct)

    • How many space groups are available for protein crystallization?

  • 32 (correct)
  • 11
  • 65
  • 230

    • Which of the following screw axes is left-handed?

  • 62
  • 32
  • 42
  • 21 (correct)

    • What is essentially plotted on the Ramachandran diagram?

    <p>Conformational energy as a function of the phi/psi angles</p> Signup and view all the answers

    Among the DNA double-helical forms, gauche-trans sugar side chains are possible in:

    <p>B-DNA</p> Signup and view all the answers

    Which statement about synchrotron radiation is false?

    <p>Allows tuning of the wavelength</p> Signup and view all the answers

    What system does the crystal class 1 belong to?

    <p>triclinic</p> Signup and view all the answers

    How many Bravais lattices are there in the triclinic system?

    <p>1</p> Signup and view all the answers

    Tridymite and cristobalite are polymorphic forms of silicon.

    <p>True</p> Signup and view all the answers

    What is the orientation of the glycosidic bonds in Z-DNA?

    <p>syn</p> Signup and view all the answers

    What crystal class does the space group P6(4)22 belong to?

    <p>6/m mm</p> Signup and view all the answers

    What is aminoacyl-tRNA synthetase?

    <p>An enzyme that attaches the correct amino acid to its corresponding tRNA.</p> Signup and view all the answers

    The first crystallographic determination of a protein structure was made for:

    <p>Myoglobin (John Kendrew)</p> Signup and view all the answers

    What system does a crystal belong to if it brightens the field in one orientation but brightens it as many as four times in another orientation?

    <p>tetragonal, trigonal, or hexagonal</p> Signup and view all the answers

    Find the true statement:

    <p>the information about the three-dimensional structure of biomolecules has been derived mainly from crystallographic studies</p> Signup and view all the answers

    Find the false statement about the up-and-down barrel:

    <p>It has hydrophilic core</p> Signup and view all the answers

    Who and when discovered the structure of the DNA double helix?

    <p>Francis Crick &amp; James Watson, 1953</p> Signup and view all the answers

    What is the diameter (in Å) of B-DNA double helix?

    <p>20</p> Signup and view all the answers

    The conformational difference between A-DNA and B-DNA lies in:

    <p>sugar conformation</p> Signup and view all the answers

    How many different amino acids are proteins built from?

    <p>20</p> Signup and view all the answers

    What is Nicol's prism used for?

    <p>to polarize light</p> Signup and view all the answers

    Can natural proteins crystallize in the crystal class 222?

    <p>Yes, but only in very rare cases</p> Signup and view all the answers

    Find the false statement about small proteins (up to 100 amino acids):

    <p>They can only exist in oligomeric form</p> Signup and view all the answers

    What is the wavelength (Å) of the characteristic X-ray radiation generated from a copper tube?

    <p>1.54</p> Signup and view all the answers

    A typical N...O distance in N-H...O hydrogen bonds is:

    <p>1.5</p> Signup and view all the answers

    What is the conformation of the sugar rings in double helical B-DNA?

    <p>C2'-endo</p> Signup and view all the answers

    What symmetry element and in what location is represented by the following transformation: x,y,z -> -x,-y,z

    <p>a dyad (2) along z</p> Signup and view all the answers

    What is the fraction of RNA in ribosome mass?

    <p>50%</p> Signup and view all the answers

    How many crystallographic systems are missing from this list: monoclinic, orthorhombic, tetragonal, trigonal, hexagonal?

    <p>1</p> Signup and view all the answers

    The image plate operates on the principle of:

    <p>Photostimulated luminescence</p> Signup and view all the answers

    Which system does the crystal class 3 belong to?

    <p>triclinic</p> Signup and view all the answers

    Radiation of one wavelength is called:

    <p>monochromatic</p> Signup and view all the answers

    Which is false?

    <p>Single-domain proteins cannot form quaternary structure</p> Signup and view all the answers

    Hydrophobic groups in water tend to cluster together because:

    <p>This way more water can be released to the disordered bulk</p> Signup and view all the answers

    Which of the rays, Ordinary (O) or Extraordinary (E), is polarized in uniaxial crystals in the plane of the propagation direction and the optic axis?

    <p>E</p> Signup and view all the answers

    Which of the glide planes cannot appear as normal to x?

    <p>a</p> Signup and view all the answers

    The arrangement of simpler structural motifs in the three-dimensional protein structure is known as:

    <p>secondary structure</p> Signup and view all the answers

    Which is true about the Four-helix bundle in the globin fold?

    <p>Four-helix bundle is part of the globin fold</p> Signup and view all the answers

    Which of the following amino acids contains sulfur?

    <p>Cysteine</p> Signup and view all the answers

    What is the orientation of the side chains in Z-DNA?

    <p>pyrimidines: gauche-gauche, purines: gauche-trans</p> Signup and view all the answers

    How many protein structures have been determined by the X-ray diffraction method?

    <p>over 10,000</p> Signup and view all the answers

    The conformation of the glycosidic bond is defined as:

    <p>gauche-trans</p> Signup and view all the answers

    What lattice centering are the following nodes characteristic of: 0,0,0; 1/2,1/2,0; 1/2,0,1/2; 0,1/2,1/2?

    <p>I</p> Signup and view all the answers

    What system does the crystal class 422 belong to?

    <p>tetragonal</p> Signup and view all the answers

    What is the conformation of the 2'-deoxyribose rings in Z-DNA?

    <p>pyrimidines: C2'-endo, purines: C3'-endo</p> Signup and view all the answers

    One of the point groups below includes two-fold rotation. Which one?

    <p>-1</p> Signup and view all the answers

    What is the relative orientation of the polarization directions of the Ordinary and Extraordinary rays?

    <p>perpendicular</p> Signup and view all the answers

    What system does the crystal class 6/m mm belong to?

    <p>hexagonal</p> Signup and view all the answers

    Which of the proteins has alpha/beta structure?

    <p>Triosephosphate isomerase</p> Signup and view all the answers

    On an alanine molecule viewed along the N->Cα direction, the substituents at the Cα atom form a clockwise sequence: H-> CH3 -> CO. What stereoisomer is this?

    <p>D</p> Signup and view all the answers

    Study Notes

    Proteins and Nucleic Acids

    • A bacterial ribosome (E. coli) has 53 proteins.
    • The four-helix bundle is a globin fold, and its helices are antiparallel.
    • Cysteine is an amino acid that contains sulfur.
    • In Z-DNA, the side chains are oriented in a gauche-gauche conformation for pyrimidines and gauche-trans for purines.
    • Over 10,000 protein structures have been determined by the X-ray diffraction method.

    Crystals and Symmetry

    • The crystal class 422 belongs to the tetragonal system.
    • In orthorhombic, monoclinic, and triclinic crystals, light is not split into two rays in any direction.
    • The crystal class 1 belongs to the triclinic system.
    • The crystal class 6/m mm belongs to the hexagonal system.
    • In a cubic system, crystals are not uniaxial.
    • Nicol's prism is made of calcite.

    Protein Structure

    • The alpha helix region is located in the upper left quadrant of the Ramachandran Plot.
    • The alpha helix has a dipole moment, and its surface can have a hydrophobic side and a hydrophilic side.
    • The smallest amino acid is glycine.
    • Gamma-crystallin has an alpha/beta structure.
    • Triosephosphate isomerase has an alpha/beta structure.
    • Papain has an alpha/beta structure.

    Nucleic Acids

    • The distance between the planes of the successive base pairs stacked in the B-DNA double helix is 3.4 Å.
    • In Z-DNA, the glycosidic bonds are in the syn conformation.
    • In A-RNA, the ribose is in the C3'-endo conformation.
    • In most forms of nucleic acids, the glycosidic bonds are anti.
    • The syn form of the glycosidic bond has been observed in purine-ribose and pyrimidine-ribose nucleotides.
    • In DNA, the cis peptide bonds are most likely to be found between proline and any other amino acid.

    Light and Optics

    • The range of wavelengths in the visible light is 400-700 Å.
    • In linearly polarized light, the electric vector vibrates in one plane.
    • In unpolarized light, the electric and magnetic vectors are perpendicular to each other.

    Miscellaneous

    • Linus Pauling discovered the alpha helix.
    • The pitch of the A-DNA double helix is 26.0 Å.
    • In Z-DNA, the glycosidic bonds are oriented in a gauche-gauche conformation for pyrimidines and gauche-trans for purines.
    • Tridymite and cristobalite are polymorphic forms of silicon.
    • An anticodon is a triplet of nucleotides (in tRNA) that is complementary to a codon.### Crystal Structure and Symmetry
    • 230 three-dimensional point groups (crystal classes) exist
    • Orthorhombic, monoclinic, and triclinic crystals have no optic axes
    • The "corn" rule relates to the absolute configuration of amino acids
    • The directionality of the peptide chain determines syn or anti glycosidic bonds in DNA
    • Sugar conformation is different in A-DNA and B-DNA
    • B-DNA has a diameter of 20 Å

    DNA Structure

    • Z-DNA has left-handed, syn glycosidic bonds
    • A-DNA has a diameter of 26 Å, and sugar conformation is C2'-endo, glycosidic bonds are anti, and side chains are gauche-gauche
    • B-DNA has a diameter of 20 Å
    • Z-DNA has a pitch of 45 Å
    • A-DNA has a pitch of 28.2 Å
    • B-DNA has a pitch of 33.4 Å

    Protein Structure

    • The first three-dimensional protein structure was determined for myoglobin
    • The first crystallographic determination of a protein structure was made for hemoglobin
    • Aminoacyl-tRNA synthetase is an enzyme attaching an amino acid to the 5'-end of a corresponding tRNA molecule
    • Proteins can crystallize in the crystal class 222
    • Small proteins (up to 100 amino acids) are usually unable to form stable hydrophobic cores
    • Fatty-acid binding proteins have an up-and-down barrel structure

    Crystallography

    • The solvent content, by volume, in protein crystals is usually 30 - 80%
    • Sodium azide is used as an antibacterial agent during protein crystallization
    • The valence angles around a C(sp3) atom are 109.5°
    • Repeated peptide units having phi=-119 deg and psi =113 deg will form an alpha helix
    • Repeated peptide units having phi=-139 deg and psi=135 deg will not form a regular secondary structure
    • Repeated peptide units having phi=-57 deg and psi=─47 deg will form an alpha helix

    Other

    • 65 space groups are available for protein crystallization
    • There are 3 RNA molecules in the small ribosomal subunit
    • There are 6 RNA molecules in the large ribosomal subunit
    • Nicol's prism is used to polarize light### Chirality and Molecular Structure
    • The absolute configuration of a chiral molecule can be defined through torsion angles.
    • The absolute value of any torsion angle must be less than or equal to 180 degrees.

    Amino Acids and Proteins

    • Tryptophan is the largest amino acid with the most non-H atoms.
    • The alpha helix has a handedness in the N->C direction that is opposite to that in the C->N direction.
    • The hydrogen bonds within an alpha helix are formed between the N-H group of unit n and the C=O group of unit n+4.
    • The C=O groups in an alpha helix point in the C->N direction.
    • Myoglobin does not have quaternary structure.
    • Hemoglobin does have quaternary structure.

    Crystallography

    • There are 14 Bravais lattices.
    • The crystal class 32 belongs to the cubic system.
    • The crystal class 23 belongs to the trigonal system.
    • The space group I2(1)3 belongs to the monoclinic system.
    • The crystal class 3 belongs to the trigonal system.
    • The crystal class 4 does not exist.
    • The direct lattice vector is normal to the b* and c* vectors of the reciprocal lattice.
    • The Ewald construction is used to illustrate the structure factor in the complex plane.

    Nucleic Acids

    • A typical tRNA molecule has 75 nucleotides.
    • Poly(dG.dC) crystallized from high ionic strength has the form Z-DNA.
    • The form of double-helical RNA is A-RNA.
    • The number of base pairs per one helical turn of the B-DNA double helix is 10.
    • The pitch of the B-DNA double helix is 33.8 Å.
    • The conformation of the sugar rings in double helical B-DNA is C2'-endo.

    X-ray Radiation

    • The wavelength of the characteristic X-ray radiation generated from a copper tube is 1.5 Å.
    • Radiation of one wavelength is called monochromatic.

    Protein Crystallization

    • Protein crystallization requires the formation of crystallization nuclei in the metastable region and their growth in the labile region.
    • The hanging-drop method is used to form protein crystals in the drop.

    Bond Lengths and Angles

    • A typical single C-C bond in organic molecules has a length of 1.52 E-10 cm.
    • A typical Mg-O coordinative bond has a length of 3.6 Å.
    • A typical N...O distance in N-H...O hydrogen bonds is 2.7 Å.

    Hydrophobic Groups and Water

    • Hydrophobic groups in water tend to cluster together because their ordered structure is favored entropically.

    Optics

    • Ordinary (O) rays are polarized in the plane of the propagation direction and the optic axis in uniaxial crystals.

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