Exam 1- Proteins

Question 1

Peptides

Answer 1

Moderate chain length connected by peptide bonds. Rigid due to tautomerism, other bonds free to rotate about axis. Some peptides are biologically active like hormones.

Question 2

Functions of proteins (5)

Answer 2

Structural roles in the body, enzymes, contractile structures, transport Hb, and transport other molecules

Question 3

Solubility characteristics of proteins

Answer 3

Fibrous and Insoluble, Globular and folded into spherical structures, Fibrous and Soluble

Question 4

Examples of fibrous and insoluble proteins

Answer 4

Collagen, elastin, and alpha-keratin

Question 5

Examples of globular proteins

Answer 5

Hemoglobin and Albumin

Question 6

Examples of fibrous and soluble proteins

Answer 6

Fibrinogen

Question 7

Solubility characteristics of globular proteins

Answer 7

Spherical structures with hydrophobic interior and hydrophilic exterior. Usually soluble

Question 8

6 naturally occurring modifications of amino acid residues

Answer 8

Acetylation, carboxylation, hydroxylation, glycosylation, phosphorylation, disulfide linkages

Question 9

Describe acetylation

Answer 9

Acetylation of n-terminus resists degradation

Question 10

Describe carboxylation

Answer 10

Glutamate is carboxylated in prothrombin (clotting protein) in a vitamin K dependent reaction. Deficiency of vitamin K therefore leads to hemorrhaging.

Question 11

Describe hydroxylatiom

Answer 11

Proline structures become hydroxylated to stabilize collagen in a vitamin C dependent reaction. Therefore vitamin C deficiency leads to scurvy

Question 12

Describe glycosylation

Answer 12

Many proteins, ab’s, acquire oligosaccharides on asparagine residues

Question 13

Which amino acids undergo phosphorylation?

Answer 13

Threonine, serine and tyrosine because they all have a hydroxyl group

Question 14

Stabilization of higher order structures (4)

Answer 14

Electrostatic interactions (salt bridges ie pos and negative bonding)
Internal hydrogen bonding
Short range van der walls and London dispersion forces between neutral residues (dipole-dipole and polarizability)
Hydrophobic effect (entropy driven)

Question 15

Surface charges on proteins may arise from 7 different amino acids

Answer 15

Aspartic acid, glutamic acid
Histidine, Arginine, and Lysine
Tyrosine and cysteine- phenolate and thiolate group

Question 16

Zinc fingers

Answer 16

Zinc complexed with 4 amino acids (usually histidine and cysteine) causing a loop of 12 amino acids

Question 17

Kringle domains

Answer 17

Loop held in place by disulfide bonds

Question 18

Leucine zippers

Answer 18

Arrangements of leucine along 1 side of the alpha helix regions in 2 proteins so that the proteins can form dimers leaving basic amino acid regions to bind to DNA

Question 19

Denaturation can be reversible or irreversible (5 types)

Answer 19

1) detergents
2) chaotropic agents
3) high temperature
4) drastic pH changes
5) organic solvents

Question 20

Sickle Cell anemia

Answer 20

Alterations in the 6th amino acid in Hb changed from Glu to Val

Question 21

Alpha helix - describe structure, found in, and what can block elongation

Answer 21

Alpha helix with 3.6 aa’s per turn made by H-bonds between carbonyl o + imido group of aa 4 residues down (N+4).
Main component of hair, alpha keratin
Proline can block elongation due to its ring structure

Question 22

Beta sheets- describe structure and where it is found in

Answer 22

Perpendicular H bonds between two chains aligned anti parallel. Found in silk fibroid, beta keratin family

Question 23

Beta turn

Answer 23

Accomplishes reversals in direction, carbonyl O and N+3

Question 24

Tertiary structure

Answer 24

Each protein has it’s own unique tertiary structure. Structured regions of alpha helixes, beta pleated sheets, and beta turns folded on one another. Generally, folded hydrophobic region outside and hydrophilic regions extending out into solution. Common: alpha helix bundles, antiparallel twisted beta sheet barrels, or mixed.

Question 25

Gibb’s free energy equation (entropy driven hydrophobic effect)

Answer 25

``` G= H - TS G- Gibbs free energy H- enthalpy (heat) T- temperature S- entropy ``` Negative G- spontaneous

Question 26

Explain Hydrophic effect in regards to proteins

Answer 26

Nonpolar substances (proteins aggregate in tertiary or quaternary structures) in an aqueous solution excluding H2O molecules. Thereby, increasing order of protein. But, overall increasing entropy due to the increased disorder of water molecules. Overall increased entropy, makes Gibbs free energy more negative and therefore proteins can aggregate in a spontaneous reaction.

Question 27

Molecular Chaperone. Name them.

Answer 27

Help new polypeptide chains form secondary or tertiary structure without entanglements. At least 2 heat shock proteins (MW: 40-70 kD), TriC: T-peptide ring complex - large donut shaped chaperonin (MW: 1700 kD)

Question 28

Prions

Answer 28

Proteinaceous infectious particles, abnormal form of a normally harmless protein found in the brain, that can either be inherited, acquired, or sporadic.

Question 29

Describe the disease process of prions

Answer 29

Normally prions found in certain cells of the CNS in the “cellular form” PrPc which is alpha helix, soluble in water, and sensitive to proteases. However, through inherited, acquired, or sporadic modalities it comes in contact with the infectious or “scrapie” version which is beta sheet structure, insoluble, and protease resistant. It has been proposed that when PrPc comes in contact with PrPsc it converts to the infectious form and forms insoluble polymeric structures. Note that difference PrPc and PrPsc have same primary structure, differ in secondary structure.

Question 30

Human prion diseases

Answer 30

Creutzfeld-Jacob: mad cow disease, Bovine spongiform encephalopathy Gerstmann-Straussler-Scheinker (GSS) Fatal familial insomnia: can’t sleep until die Kuru (New Guinea tribes contracted by cannibalism of the dead)

Question 31

Quaternary structure. Proteins that have quaternary structure are said to be....

Answer 31

Polypeptide subunits held together by non-covalent forces to form oligomeric structures. Oligomeric, and can be referred to dimers or tetramers. In contrast to polypeptide chains referred to as monomers, protomers, or subunits.