Lecture 2: Protein Structure Flashcards
What are the (4) Main Fxs of Proteins
Catalysis. Transport. Structure. Motion
How do you name Amino Acids?
Begin at the Alpha-Carbon down to the R-Group
True or False
The Alpha Carbon in Amino Acids always has a chiral carbon?
True
All AA except which one have an (A) acidic carboxyl group (B) Basic Amino Group (C) Alpha Hydrogen) connected to the carbon
Proline
Name the Aromatic AA?
Tyrosine- Tryptophan- Phenylalanine
FX. of Aromatic AA
Absorb UV light at 270-180 nm
Name the Non-polar, aliphatic AA
(Glyanna and Alanna went pro but vaguely lets Isolesha Methionate)
Glycine- Alanin-Proline-Valine-Leucine-Isoleucine-Methionine
Fx. of Non-polar, aliphatic AA
Side chains are hydrophobic
Name polar, uncharged AA
(Three cysters seriously asparged glutamine_
Threonine-Cysteine- Serine- Asparganine-Glutamine
Fx polar, uncharged AA
side chains can form H+ bonds; cysteine forms disulfide bonds
Name positively charged AA
(HIs arm was Lysed)
Histidine Arginine Lysine
Fx. positively charged
Serve as proton donors/acceptors
Name negatively charged AA
(Georgeate -GA)
Glutamate Aspartate
What is twitter-ionic?
Dipole ion with spatially separated (+)/(-) charges
What are covalently linked AA
Peptides
General Term for fx. non0AA component
Cofactor
Used to designate an organic cofactor
Coenzyme
Covalently attached cofactors
Prosthetic Groups
True or False; there is no cost in conformational energy for a native fold
False; there IS a cost of conformational energy
True or False; Electrostatic Interactions- salt-bridges stabilize the protein
True
True or False; Interaction of N-H/C–O of the peptide bond leads to local regular structures such as Alpha-Helixes/Beta-Sheets
True
True of False; Protein Structure is partially dictated by the properties of the peptide bond
True
True or False; Resonance causes peptide bonds to be rigid/planar
True
Psi bond refers to which bond in AA?
Bond bt. alpha & carbonyl Carbon
Phi bond refers to which bond in AA?
Bond bt. alpha & amide Nitrogen
Intermolecular Interactions are responsible for what secondary structures
H-Bonding; carbonyl-amide of Amino Acid Groups
Will you find proline residues on a secondary structure?
If so, where
Yes; Beta-Sheets
What is an alpha helix?
Stabilized by H+ bonds between nearby residues
What is a beta sheet?
Stabilized by H+ bonds between adjacent segments that may not be nearby in primary sequence
What is random coil?
Irregular arrangement of the polypeptide chain
What is the secondary structure
Spatial arrangement of he polypeptide chain
What is the Ramachandran Plot?
Distribution of psi/phi dihedral angels in a protein (tendency of AA to interact)
What favors/disfavors interactions of AA in configuration?
Prohibit- Steric Hinderance & Repulsive Forces
Promote- H-Bonding & Attractive forces bt. atoms
In collagen, what makes up the right hand, superhelical triple helices?
3 left handed chains intertwined into “SUPER DUPER” right-handed triple helix.
Folding of a peptide to its native form is favorable or unfavorable?
unfavorable
What is the 3rd AA in B- sequence
Glycine
True or False
Alpha Helix; Backbons is NOT compact
False, it is very compact
True or False
Alpha Helix; the inner diameter is too small for anything to fit “inside”
True
True or False; Alanine & Leucine are strong helix formers
True
True or False; Proline acts as a helix breaker because the rotation around N-C alpha bond is impossible
True
True or False; Glycine as as a helix breaker because the tiny R-group supports other conformations
True
True or false; Beta Sheets; Backbone is more extended with psi dihedral between 90-180 degrees?
True
True or False; H-bonded strands run in opposite direction
False; parallel run in the same direction
What is the 2nd AA in B turn sequence?
proline
What is the tertiary structure?
Spatial arrangement of atoms in a polypeptide chain or protein
What are the (2) major classes of proteins
Fibrous Proteins/Globular Proteins
What are Fibrous Proteins?
Insoluble; made from single secondary structure
What are Globular Proteins
Water-soluble globular proteins; lipid-soluble membraneous proteins
Which collagen is the strongest and has the greatest tensile strength?
right-handed superhelical triple helix (Super-Duper)
True or False; Collagen is NOT a constituent of connective tissue
False; Collagen is a constituent of connective tissue
What makes up a collagen fibril?
Many triple-helixes
What shape do globular proteins have?
Spherical
Are Globular Proteins water soluble or insoluble?
water soluble
What causes quaternary structure?
formed by spontaneous assembly of individual polypeptides into a fx. cluster.
You extract a protein from a lipid bilayer of a cancel cell. What category of protein is this?
Globular Protein
What is the basic building block of collagen protein Alpha-Helix?
Threonine
True or False; Proteins function depends on its 3-D structure?
True
What is denaturation
Loss of structural integrity/loss
What are a few ways proteins can be denature?
pH extremes, temperature, organic solvents, chaotropic events
How many Cystein residues and disulfide bonds does Ribonuclease have?
8 Cys residues/ 4 disulfide bonds
If urea and 2-meracaptoethanol are removed, what does the protein do?
Spontaneously refold; correct disulfide bonds are reformed
What is one way enzymes speed up reactions?
Lower activation energy/coupling to a fast one
What is the underlying determinant of a tertiary structure?
Primary Structure Sequence
Keratin is made up of which proteins?
Alpha-Helices
Protein structure is determined by which sequence and what does it dictate?
Primary; dictates function of the protein
What drives the formation of a peptide’s secondary structure?
side chain interactions
What is the second turn in a Beta sheets?
Proline (I have to PEE!)
How many AA are required to complete a B-turn in a B-sheet?
4
All of the following are considered “weak” interactions in proteins, except:
A) hydrogen bonds. B) hydrophobic interactions. C) ionic bonds. D) peptide bonds. E) van der Waals forces.
D
The most important contribution to the stability of a protein’s conformation appears to be the:
A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein.
C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein.
D) sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.
E) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.
A
In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:
A) formation of the maximum number of hydrophilic interactions.
B) maximization of ionic interactions.
C) minimization of entropy by the formation of a water solvent shell around the protein.
D) placement of hydrophobic amino acid residues within the interior of the protein.
E) placement of polar amino acid residues around the exterior of the protein.
D
Pauling and Corey’s studies of the peptide bond showed that:
A) at pH 7, many different peptide bond conformations are equally probable.
B) peptide bonds are essentially planar, with no rotation about the C—N axis.
C) peptide bonds in proteins are unusual, and unlike those in small model compounds.
D) peptide bond structure is extraordinarily complex.
E) primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly.
B
In the diagram below, the plane drawn behind the peptide bond indicates the:
A) absence of rotation around the C—N bond because of its partial double-bond character.
B) plane of rotation around the Cα—N bond.
C) region of steric hindrance determined by the large C=O group.
D) region of the peptide bond that contributes to a Ramachandran plot.
E) theoretical space between -180 and +180 degrees that can be occupied by the φ and ψ angles in the peptide bond.
A
Which of the following best represents the backbone arrangement of two peptide bonds? A) Cα—N—Cα—C—Cα—N—Cα—C B) Cα—N—C—C—N—Cα C) C—N—Cα—Cα—C—N D) Cα—C—N—Cα—C—N E) Cα—Cα—C—N—Cα—Cα—C
D
Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds? A) Cα—C and N—Cα B) C=O and N—C C) C=O and N—Cα D) N—C and Cα—C E) N—Cα and N—C
A
Roughly how many amino acids are there in one turn of an α helix?
A) 1 B) 2.8 C) 3.6 D) 4.2 E) 10
C
In the α helix the hydrogen bonds:
F) are roughly parallel to the axis of the helix.
G) are roughly perpendicular to the axis of the helix.
H) occur mainly between electronegative atoms of the R groups.
I) occur only between some of the amino acids of the helix.
J) occur only near the amino and carboxyl termini of the helix.
F
In an α helix, the R groups on the amino acid residues:
A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) cause only right-handed helices to form.
D) generate the hydrogen bonds that form the helix.
E) stack within the interior of the helix.
B
Thr and/or Leu residues tend to disrupt an α helix when they occur next to each other in a protein because:
A) an amino acids like Thr is highly hydrophobic.
B) covalent interactions may occur between the Thr side chains.
C) electrostatic repulsion occurs between the Thr side chains.
D) steric hindrance occurs between the bulky Thr side chains.
E) the R group of Thr can form a hydrogen bond.
D
A D-amino acid would interrupt an α helix made of L-amino acids. Another naturally occurring hindrance to the formation of an α helix is the presence of:
A) a negatively charged Arg residue.
B) a nonpolar residue near the carboxyl terminus.
C) a positively charged Lys residue.
D) a Pro residue.
E) two Ala residues side by side.
D
An α helix would be destabilized most by:
A) an electric dipole spanning several peptide bonds throughout the α helix.
B) interactions between neighboring Asp and Arg residues.
C) interactions between two adjacent hydrophobic Val residues.
D) the presence of an Arg residue near the carboxyl terminus of the α helix.
E) the presence of two Lys residues near the amino terminus of the α helix.
E
The major reason that antiparallel β-stranded protein structures are more stable than parallel β-stranded structures is that the latter:
A) are in a slightly less extended configuration than antiparallel strands.
B) do not have as many disulfide crosslinks between adjacent strands.
C) do not stack in sheets as well as antiparallel strands.
D) have fewer lateral hydrogen bonds than antiparallel strands.
E) have weaker hydrogen bonds laterally between adjacent strands
E
Amino acid residues commonly found in the middle of β turn are: A) Ala and Gly. B) hydrophobic. C) Pro and Gly. D) those with ionized R-groups. E) two Cys.
C
A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n): A) antiparallel β sheet. B) parallel β sheet. C) α helix. D) α sheet. E) β turn.
E
The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are:
A) always side by side.
B) generally near each other in sequence.
C) invariably restricted to about 7 of the 20 standard amino acids.
D) often on different polypeptide strands.
E) usually near the polypeptide chain’s amino terminus or carboxyl terminus.
B
