What amino acid can form disulfide bridges?
cysteine
Salt bridges
strong interactions between cationic and anionic groups in a protein. Has both H-bonding and Ionic (Coulombic) interactions
Disulfide bridges
Strong covalent bonds formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer
alpha helix
A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure. Stabilized by hydrogen bonds between nearby residues.
Beta sheet
Formed by hydrogen bonds between backbone atoms on adjacent regions of the peptide backbone called beta strands. Do not involve side chains
Random coil
Irregular arrangement of the polypeptide chain.
How many residues per turn in a right-handed helix?
3.6 residues per turn
A pitch
5.4 angstrom
What is the coiled length of a polypeptide of 80 amino acid residues in a single continuous ?-helix?
120 A
What is the inner diameter of the alpha helix? (no side chains)
4-5 A
What is the outer diameter of the alpha helix? (with side chains)
10-12 A
Parallel beta sheets
H-bonded strands run in the same direction resulting in bent H-bonds (Weaker).
Anti-parallel beta sheets
The H-bonded strands run in opposite directions resulting in linear H-bonds (stronger).
Fibrous proteins
-structural function
-Strong long strands/sheets
-water insoluble
-rod like
Globular proteins
-often multiple types of secondary structures (glob-like)
-Enzymes and regulatory function (not structural)
-water soluble
silk fibroin
Fibroin is the main protein in silk from moths and spiders. It has antiparallel beta sheet structure
Collagen
an important constituent tissue. Each chain is a long Gly- and Pro- rich left handed helix. Three collagen chains intertwine to form a right-handed superhelical triple helix.
Gelatin
an example of a colloidal solution
myoglobin
an oxygen binding protein of muscle cells. Stores oxygen in muscle cells.
how many coordination sites does iron have?
6
Proteostasis
Maintenance of cellular protein activity is accomplished by the coordination of many different pathways which include chaperones and proteosomes
denaturation
loss of structural activity with accompanying loss of activity
How can proteins be denatured?
Proteins can be denatured by
-Hot or cold temperatures
-pH extremes
-chaotropic agents
-reducing agents(break disulfide bridges)
Chaotropic agents
disrupts the structure and denatures the DNA by increasing the entropy and non-covalent forces like hydrogen bonds (Ex. urea)
Urea is a ________ agent
chaotropic
2-Mercaptoethanol is a __________ agent
reducing
Chaperons
-proteins that help large polypeptide chains that usually have multiple folding domains, to fold properlly
Amyloidoses
formation of abnormal misfolded long fibrillar proteins with mainly beta pleated sheets called amyloids.
Prion
Protein-aceous infectious
Electrophoresis
method of separating proteins by electrical charge
SDS
sodium dodecyl sulfate, a detergent
What are the two ways to determine DNA sequence?
Edman degradation (Classical method), and Mass spectrometry (Modern method)
Proteases
proteins that act as enzymes to break apart other proteins
The amino acid sequence of myoglobin is __________ structure
primary
The C helix of alpha-lactalbumin is _______ structure
secondary
myoglobin with heme is ________ structure
tertiary
hemoglobin is ________ structure
Quaternary
Alpha helices are a type of secondary structure in proteins. What is the length of a 25-kDa single-stranded ?-helical protein segment? Assume a mean residue mass of 110 Da
341 A
How many Angstroms per residue in a alpha helix?
1.5 A/residue
What does the primary structure of a protein refer to?
A) The presence of an ? helix
B)The ?-amino acid sequence in the polypeptide chain
C)The orientation of the side chains in three-dimensional space
D)The presence of cross-links with disulfide bonds
B)The ?-amino acid sequence in the polypeptide chain
How many angstroms per residue in an antiparallel beta sheet?
3.5A/residue
How many angstroms per residue in a parallel beta sheet?
3.25A/residue
Select the true statements about secondary structure
A)In a ?-pleated sheet, the side chains extend above and below the sheet
B)In an ?-helix, the side chains are located inside the helix
C)The ?-helix is held together by hydrogen bonds between the amide
A)In a ?-pleated sheet, the side chains extend above and below the sheet
C)The ?-helix is held together by hydrogen bonds between the amide N-H and C=O groups
D)The secondary level of protein structure refers to the spatial arrangements of short segments
What is the major force controlling tertiary protein structure?
hydrophobic effect
In the alpha-helix, where do the hydrogen bonds occur?
the hydrogen bonds occur between the n and n+4 amino acids of the helix
Amino acid residues commonly found in the middle of B-turns are _________
Proline (Pro) and Glycine (Gly)
What are the steps in hair waiving(perm)?
reduce--->curl (shape hair)--->oxidize
Which of the following statements is false?
A. Collagen is a protein in which the polypeptides are mainly in the ?-helix conformation.
B. Disulfide linkages are important for keratin structure.
C. Gly and Pro residues are particularly abundant in collagen
A. Collagen is a protein in which the polypeptides are mainly in the ?-helix conformation.
Protein S will fold into its native conformation only when protein Q is also present
in the solution. However, protein Q can fold into its native conformation without
protein S. Protein Q, therefore, may function as a ____________ for protein S.
A. protea
B. molecular chaperone
8. What is the advantage of adding SDS to gel electrophoresis?
A. SDS colors the proteins for visualization.
B. SDS reduces disulfide bonds.
C. SDS allows proteins to be separated on the basis of approximate mass by adding excess negative charge
D. None o
C. SDS allows proteins to be separated on the basis of approximate mass by adding excess negative charge
9. Two-dimensional electrophoresis is a combination of what two techniques?
A. isoelectric focusing and affinity chromatography
B. ion-exchange chromatography and SDS-PAGE
C. affinity chromatography and SDS-PAGE
D. isoelectric focusing and SDS-PAGE
E. iso
D. isoelectric focusing and SDS-PAGE