Protein - Biochemistry

Question 1

What are the nonpolar (hydrophobic) amino acids?

Answer 1

1) proline (pro, P)
2) Glycine (gly, G)
3) alanine (ala, A)
4) valine (Val, V)
5) leucine (Leu, L)
6) isoleucine (ILE, I)
7) phenylalanine (Phe, “F”)
8) methionine (Met, M)
9) tryptophan (Trp, “W”)

Question 2

What are the polar, neg charged amino acids? (hydrophilic, acidic in the protonated state?

Answer 2

1) aspartate (Asp, “D”)
2) glutamate (Glu, “E”)

negatively charged at physiologic pH, present as conjugate bases (therefore are –ate not –ic acid)

Question 3

What are the polar positively charged amino acids? (Hydrophilic, basic in the unprotonated state)

Answer 3

1) histidine (His, H)
2) lysine (lys, “K”)
3) arginine (arg, “R”)

Question 4

What are the polar, neutral (hydrophilic) amino acid?

Answer 4

1) serine (Ser, S)
2) asparagine (asn, “N”)
3) threonine (Thr, T)
4) Glutamine (Gln, “Q”)
5) Tyrosine (Tyr, “Y”)
6) Cysteine (cys, C)

Question 5

what are the pKa values of alpha-amino and alpha-carboxy groups of amino acids.

Answer 5

carboxyl - ~2.2
amino - ~9.4

note: at physiological pH, amino acids are zwitterion

Question 6

what is the only amino acid that is achiral?

Answer 6

glycine because it has 2 hydrogen atoms

Question 7

which amino acid is both hydrophobic and hydrophilic?

Answer 7

tyrosine. The benzene group makes it hydrophobic, and the phenolic group

Question 8

what are the aromatic amino acid? what are the characteristics?

Answer 8

phenylalanine, tyrosine, tryptophan.

1) very hydrophobic
2) Absorb UV at 280 nm

Question 9

what is the only cyclic “imino acid”?

Answer 9

proline

Question 10

Which amino acid functions as buffer in physiologic range?

Answer 10

Histidine

Question 11

what part of the peptide determines the overall charge?

Answer 11

the side chain determines the overall charge because in making peptide bond, the charge in amino and carboxyl groups is destroyed (maybe a test questions). Amide linkage are neutral.

Question 12

what is a pI?

Answer 12

pI, also known as isoelectric point, is the pH at which the number of positive and negative charges on a population of molecules is equal, so no net charge.

Question 13

what is the formula for the pI of a neutral amino acid?

Answer 13

pka(C alpha) + pKa(N alpha)
pI (isoelectric) = ——————-
2

Question 14

what is the formula for pI of an acidic amino acid?

Answer 14

pka(C alpha) + pKa(C side chain)
pI = ——————-
2

this is for glutamate and aspartate

Question 15

what is the formula for pI of an basic amino acid?

Answer 15

pka(N alpha) + pKa(N side chain)
pI = ——————-
2

Question 16

what is a protein?

Answer 16

a functional polypeptide with a biological role (native protein). sometimes contains non-polypeptide (prosthetic group, coenzyme, cofactor) portions. very small protein are often hormones (such as insulin).

Question 17

what are the rules for reading a peptide chain?

Answer 17

1) Repeating unit N-C-C
2) Read from N or amino terminal residue always on left, carboxyl terminal residue on right
3) Residue = an amino acid in a peptide

Question 18

what is a peptide bond?

Answer 18

• The amide linkage between a carboxyl group on one amino acid that is covalently bonded to the amine group on another.
• an endergonic reaction, requiring energy.
• condensation reaction with water as a one of the products.
• Hydrolysis (addition of water to cleave) peptide bond are favored energetically, but are very slow, unless it is catalyzed by strong mineral acid (HCl) or high temperature.
• Amino acids must be “activated”by ATP-driven reactions to be incorporated into proteins
• peptide bonds are single bond, with 40% double bond character so the bond length is usually 1.33 Angstrom

Question 19

what configuration (cis, trans) are peptide bonds mostly in?

Answer 19

Peptide bonds are planar, mostly in trans configuration.

cis configurations are limited to proline.

Question 20

what are simple proteins?

Answer 20

Composed only of amino acid residues

Question 21

what are conjugated proteins?

Answer 21

contains prosthetic groups (metal ions, co-factors, lipids, carbohydrates). Examples: in hemoglobin, heme prosthetic group.

Question 22

what are fibrous protein?

Answer 22

1) polypeptides arranged in long strands or sheets
2) water insoluble (lots of hydrophobic amino acid)
3) strong but flexible
4) structural (alpha keratin, collagen)

Question 23

what are globular (spherical) proteins?

Answer 23

1) polypeptide chains folded into spherical or globular form
2) water soluble
3) contain several types of secondary structure
4) diverse functions (enzymes, regulatory protein)

Question 24

what is a primary structure?

Answer 24

The genetically encoded sequence of amino acids in a peptide or polypeptide chain starting at the N-terminal end and going to the C-terminal end.

Question 25

what are secondary structures?

Answer 25

the 3-d shape of a protein chain that results form hydrogen bonding between peptide bonds on the polypeptide chain.

1) alpha helix (most abundant)
2) beta pleaded sheets

*secondary structures describe the overall folding of the primary structures.

Question 26

what are tertiary structures?

Answer 26

tertiary structures are the overall folding of the secondary structures. the secondary structures are called domain in a tertiary structures. tertiary is the highest structure a single polypeptide can attain

Question 27

what are quaternary structures?

Answer 27

interaction of tertiary structures such as hemoglobin

Question 28

what are the major common post-translational modifications after the protein is synthesize and leaves the ribosome?

Answer 28

1) hydroxylation - hydroxyproline and hydroxylysine which stabilizes collagen
2) addition Pi (phosphate)group onto ser, the
3) addition of sugars to give glycoproteins (prion protein)
4) disulfide bond formation

Question 29

what is the difference between configuration and conformation?

Answer 29

Configuration are different geometries due to orientation in space (cis/trans, D/L, R/L), cannot switch between configuration without breaking bonds. In terms of thermodynamics, native proteins would be found in its most stable and energetically favorable configuration in its biologically active state.

Conformation are alternate arrangements that arise from molecular motion (chair vs boat), can switch around freely

Question 30

What stabilizes alpha helix?

Answer 30

Intramolecular hydrogen bonding.

Note: all hydrogen bonds in the alpha helix are oriented in the same direction giving the helix a dipole with the N-terminus being positive and the C-terminus being negative

Question 31

which amino acids disrupts the polypeptide chain in alpha helix?

Answer 31

1) proline - no hydrogen on the Nitrogen for hydrogen bonding. The ring “natural” rotation of chain is disrupted.
2) Glycine - has 2 hydrogen which allows for too much free rotation (no side chain group)
3) ser, asp, asn -interfering H-bonding
4) ile, val - steric effect. disrupts helix formation because of bulky side chains

Question 32

what are keratins?

Answer 32

• structural fibrous proteins
• major protein found in hair and fingernails and animal skin.
• contains a large amount of cysteine, required for disulfide bridges. Disulfide bonds resist forces tending to deform them.
• 2 properties: insolubility and resistance to stretching
• the more cys residues, the more disulfide (covalent) bonds, the harder the keratin (nails have numerous disulfide bridges. less cysteines, the hair is more curly because of lesser disulfide bonds)

Question 33

what are beta pleated sheets?

Answer 33

• intermolecular hydrogen bonding of peptide bonds stacked on top of each other.
• chains may be parallel or antiparallel (antiparallel configuration is more stable).
• h-bonding are perpendicular to the polypeptide chains
• no regular repeating pattern as in alpha helix

Question 34

Give examples of the function of collagen.

Answer 34

(hint: collagen mean “forming glue” in greek, therefore means that collagen holds most animals together. The triple helix structure of collagen makes it strong)
1) form the matrix, or cement, material in bone, on which the mineral constituents precipitate.
2) major portion of tendons
3) skin

Question 35

What is the Prolyl Hydroxylase and lysyl hydroxylase? (possible test question)

Answer 35

Prolyl Hydroxylase and lysyl hydroxylase are enzymes that catalyzes the hydroxylation (adding hydroxyl (-OH) group) to the Proline and Lysine to become Hydroxylproline and Hydroxylysine.

Question 36

What is hydroxyproline for?

Answer 36

Critical for collagen stability. The hydroxyl group greatly increases H-bonding between chains, which stabilizes the chains.

Question 37

What is scurvy?

Answer 37

A condition caused by lack of collagen. Symptoms include loss of teeth and degeneration of connective tissues. Caused by lack of ascorbic acid (vitamin C) in diet, which slows the production of hydroxyproline and stops the construction of collagen

Question 38

What are the 5 classes of tertiary interactions/bonds?

Answer 38

reversible, nonbonding interaction

1) hydrophobic forces (attraction)
2) Van der Waals interaction
3) side chain H-bonding
4) salt linkage

covalent bonds (can only be broken down by reduction)

5) disulfide linkage

Question 39

what are hydrophobic interactions?

Answer 39

Interaction formed between side chains of non-polar residues (Aliphatic-ala, val, leu, ile, pro, gly and aromatic -phe, Trp, Tyr) in the interior of the protein, away from water. This interaction is not pH dependent and does not require specific orientation like an H-bond.

Note that tyrosine is considered hydrophilic in this class

Question 40

What is Side chain hydrogen bonding?

Answer 40

Hydrogen bonding between side chains of amino acid residues. Need a Hydrogen-bond donor (H-N or H-O) and an Hydrogen-bond acceptor (N or O)

pH dependent for ionizable group

Needs specific orientation (linear)

Question 41

What are ionic (salt) interactions?

Answer 41

Forms between 2 charged side chains, one negative charge and one positive charge ions. These bonds occur at the exterior of the protein.

Question 42

What are disulfide bonds?

Answer 42

stabilizes the native structure after the protein is formed and leaves the ribosome. disulfide bonds formation occurs in the endoplasmic reticulum. this is a post translation modification.

-strong covalent bond
-results of the oxidations of two cysteine that were in close proximity in folded protein
-cannot be broken down by changing temperature and pH (between 1-13)
can be broken by addition of reducing agent that converts cystine back to two cysteine

Question 43

what are quaternary structures?

Answer 43

interaction between at least 2 tertiary structures interacting. associates with other polypeptides, biopolymers, small organic/inorganic molecules

classes of bonds:

1) electrostatic or ionic (salt)
2) hydrogen bond(H with O, N, or S)
3) hydrophobic interactions
4) disulfide (infrequent)

Question 44

what are chaperonins?

Answer 44

promote protein folding and prevent misfolding of proteins

Question 45

what is denaturation of protein?

Answer 45

destroy the function of a biologic unit by destroying the nonbonding interaction. affects on secondary, tertiary,quaternary but primary structures remain intact

Question 46

what is CJD?

Answer 46

CJD or creutzfeld-jacob disease is an infectious disease that resulted from aggregates forming from mis-folded protein. Characterize by loss of motor control, dementia, paralysis wasting and eventual death. Symptoms may develop with a year.

Question 47

What is PrPc?

Answer 47

• Called PrPc (for cellular), found mostly on CNS
• A normal transmembrane glycoprotein with unknown function
• binds Cu2+ (regulates its homeostasis)
• easily digested by proteases (proteinase K)
• encoded by PRNP gene, located on human chromosome 20
• monomeric, soluble

Question 48

What is Alzheimer’s disease?

Answer 48

progressive neurodegenerative disease characterize by memory loss, impaired visuo-spatial skills, poor judgement.

Question 49

What is a spongiform encephalopathies?

Answer 49

• disease agent is protein, a “prion”
• brain looks like a sponge, (spongy degeneration)
• diagnosis done on post-mortem
• long latency period between exposure to the disease agent and clinical disease

Question 50

What is PrPsc?

Answer 50

• Proteinaceous infectious particle with no DNA or RNA detected.
• Smaller than smallest known virus.
• Not yet characterized.
• PrPsc is an abnormal prion. (sc stands for scrapie).
• Has the same amino acid sequence and primary structure as normal protein. However, the secondary structure are dominated by beta conformation.
• when PrPsc gets in contact with PrPc, it converts the PrPc to the abnormal form, and then forms aggregates.
• Insoluble but to strongest solvents
• multimeric and Resistant to digestion by proteases, survises in tissues post-mortem
• Resistant to heat, sterilization, sunlight
• No detectable immune response.

Question 51

What is an amyloid plaque?

Answer 51

An amyloid plaque in Alzheimer’s is a tangle of protein filament, which is derived from the proteolytic cleavage of amyloid precursor protein (APP). Amyloid protein changes into beta conformation forming aggregates similar to Prion.