Chapter 4 Biochemistry

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.

SDS

sodium dodecyl sulfate, a detergent

Salt bridges

strong interactions between cationic and anionic groups in a protein. Has both H-bonding and Ionic (Coulombic) interactions

myoglobin with heme is ________ structure

tertiary

myoglobin

an oxygen binding protein of muscle cells. Stores oxygen in muscle cells.

A pitch

5.4 angstrom

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

Gelatin

an example of a colloidal solution

Amyloidoses

formation of abnormal misfolded long fibrillar proteins with mainly beta pleated sheets called amyloids.

Globular proteins

-often multiple types of secondary structures (glob-like) -Enzymes and regulatory function (not structural) -water soluble

Chaperons

-proteins that help large polypeptide chains that usually have multiple folding domains, to fold properlly

Fibrous proteins

-structural function -Strong long strands/sheets -water insoluble -rod like

How many Angstroms per residue in a alpha helix?

1.5 A/residue

What is the outer diameter of the alpha helix? (with side chains)

10-12 A

What is the coiled length of a polypeptide of 80 amino acid residues in a single continuous α-helix?

120 A

How many angstroms per residue in a parallel beta sheet?

3.25A/residue

How many angstroms per residue in an antiparallel beta sheet?

3.5A/residue

How many residues per turn in a right-handed helix?

3.6 residues per turn

Alpha helices are a type of secondary structure in proteins. What is the length of a 25-kDa single-stranded α-helical protein segment? Assume a mean residue mass of 110 Da

341 A

What is the inner diameter of the alpha helix? (no side chains)

4-5 A

Select the true statements about secondary structure A)In a β-pleated sheet, the side chains extend above and below the sheet B)In an α-helix, the side chains are located inside the helix C)The α-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 of the protein E)Peptide bonds stabilize secondary structure

A)In a β-pleated sheet, the side chains extend above and below the sheet C)The α-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 of the protein

Which of the following statements is false? A. Collagen is a protein in which the polypeptides are mainly in the α-helix conformation. B. Disulfide linkages are important for keratin structure. C. Gly and Pro residues are particularly abundant in collagen. D. Silk fibroin is a protein in which the polypeptide is almost entirely in the β conformation. E. α-keratin is a protein in which the polypeptides are mainly in the α-helix conformation.

A. Collagen is a protein in which the polypeptides are mainly in the α-helix conformation.

What does the primary structure of a protein refer to? A) The presence of an α helix B)The α-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 α-amino acid sequence in the polypeptide chain

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. proteasome B. molecular chaperone C. protein precursor D. structural motif E. supersecondary structural unit

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 of the above E. All of the above

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. isoelectric focusing and ion-exchange chromatography

D. isoelectric focusing and SDS-PAGE

What are the two ways to determine DNA sequence?

Edman degradation (Classical method), and Mass spectrometry (Modern method)

silk fibroin

Fibroin is the main protein in silk from moths and spiders. It has antiparallel beta sheet structure

Beta sheet

Formed by hydrogen bonds between backbone atoms on adjacent regions of the peptide backbone called beta strands. Do not involve side chains

Parallel beta sheets

H-bonded strands run in the same direction resulting in bent H-bonds (Weaker).

Random coil

Irregular arrangement of the polypeptide chain.

Amino acid residues commonly found in the middle of B-turns are _________

Proline (Pro) and Glycine (Gly)

Prion

Protein-aceous infectious

How can proteins be denatured?

Proteins can be denatured by -Hot or cold temperatures -pH extremes -chaotropic agents -reducing agents(break disulfide bridges)

hemoglobin is ________ structure

Quaternary

Disulfide bridges

Strong covalent bonds formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer

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.

Anti-parallel beta sheets

The H-bonded strands run in opposite directions resulting in linear H-bonds (stronger).

Urea is a ________ agent

chaotropic

What amino acid can form disulfide bridges?

cysteine

Chaotropic agents

disrupts the structure and denatures the DNA by increasing the entropy and non-covalent forces like hydrogen bonds (Ex. urea)

What is the major force controlling tertiary protein structure?

hydrophobic effect

denaturation

loss of structural activity with accompanying loss of activity

Electrophoresis

method of separating proteins by electrical charge

The amino acid sequence of myoglobin is __________ structure

primary

Proteases

proteins that act as enzymes to break apart other proteins

What are the steps in hair waiving(perm)?

reduce--->curl (shape hair)--->oxidize

2-Mercaptoethanol is a __________ agent

reducing

The C helix of alpha-lactalbumin is _______ structure

secondary

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