Bio/BioChem Flashcards
“The hydroxyl groups of serine, threonine, and tyrosine residues are often modified by the attachment of a phosphate group by a regulatory enzyme called a
Kinase
“The result is a change in structure due to the very hydrophilic phosphate group. This modification is an important means of regulating protein activity.”
Histidine is a readily available proton acceptor or donor, explaining its prevalence at
protein active sites”
“Cysteine, which contains a thiol (also called a sulfhydryl—like an alcohol that has an S atom instead of an O atom), is actually fairly _____, and methionine, which contains a thioether (like an ether that has an S atom instead of an O atom) is fairly ______.”
Polar; Nonpolar
What are the two common types of covalent bonds between amino acids in proteins:”
“the peptide bonds that link amino acids together into polypeptide chains and disulfide bridges between cysteine R-groups.”
“In a polypeptide chain, the N–C–C–N–C–C pattern formed from the amino acids is known as _____. An individual amino acid is termed a ______ when it is part of a polypeptide chain.”
the backbone of the polypeptide; Residue
“At equilibrium, which is thermodynamically favored: the dipeptide or the individual amino acids”
“The dipeptide has a higher free energy, so its existence is less favorable. In other words, existence of the chain is less favorable than existence of the isolated amino acids.”
If AA is favorable over dipeptides, how are dipeptides maintained?
“During protein synthesis, stored energy is used to force peptide bonds to form. Once the bond is formed, even though its destruction is thermodynamically favorable, it remains stable because the activation energy for the hydrolysis reaction is so high. In other words, hydrolysis is thermodynamically favorable but kinetically slow.”
“Hydrolysis of a protein by another protein is called ______, and the protein that does the cutting is known as a ________
proteolysis or proteolytic cleavage; proteolytic enzyme or protease.”
“Based on the above, if the following peptide is cleaved by trypsin, what amino acid will be on the new N-terminus and how many fragments will result: Ala-Gly-Glu-Lys-Phe-Phe-Lys?”
“Trypsin will cleave on the carboxyl side of the Lys residue, with Phe on the N-terminus of the new Phe-Phe-Lys fragment. There will be two fragments after trypsin cleavage: Phe-Phe-Lys and Ala-Gly-Glu-Lys.”
“The disulfide bridge plays an important role in stabilizing _____ protein structure;”
Tertiary
“Which is more oxidized, the sulfur in cysteine or the sulfur in cystine?”
“The sulfur in cysteine is bonded to a hydrogen and a carbon; the sulfur in cystine is bonded to a sulfur and a carbon. Hence, the sulfur in cystine is more oxidized.”
“The inside of cells is known as a reducing environment because cells possess antioxidants (chemicals that prevent oxidation reactions). Where would disulfide bridges be more likely to be found, in extracellular proteins, under oxidizing conditions, or in the interior of cells, in a reducing environment?”
“In a reducing environment, the S-S group is reduced to two SH groups. Disulfide bridges are found only in extracellular polypeptides, where they will not be reduced.
Examples of protein complexes held together by disulfide bridges include antibodies and the hormone insulin.”
“Proteins are denatured by
urea (which disrupts hydrogen bonding interactions), by extremes of pH, by extremes of temperature, and by changes in salt concentration (tonicity).”
“The bond which determines 1ο structure is the ______, simply because this is the bond that links one amino acid to the next in a polypeptide.”
peptide bond
“The unique structure of _______ forces it to kink the polypeptide chain; hence proline residues never appear within the α-helix.”
Proline
“If a single polypeptide folds once and forms a β-pleated sheet with itself, would this be a parallel or antiparallel β-pleated sheet?
“It would be antiparallel because one participant in the β-pleated sheet would have a C to N direction, while the other would be running N to C.”
“What effect would a molecule that disrupts hydrogen bonding, e.g., urea, have on protein structure?
“Putting a protein in a urea solution will disrupt H-bonding, thus disrupting secondary structure by unfolding α-helices and β-sheets. It would not affect primary structure, which depends on the much more stable peptide bond. Disruption of 2°, 3°, or 4° structure without breaking peptide bonds is denaturation.”
“Ribonuclease has eight cysteines that form four disulfides bonds. What effect would a reducing agent have on its tertiary structure?”
“The disulfide bridges would be broken. Tertiary structure would be less stable.”
“Would a protein end up folded normally if you (1) first put it in a reducing environment, (2) then denatured it by adding urea, (3) next removed the reducing agent, allowing disulfide bridges to reform, and (4) finally removed the denaturing agent?”
“No. If you allow disulfide bridges to form while the protein is still denatured, it will become locked into an abnormal shape.”
“What if you did the same experiment but in this order: 1, 2, 4, 3? You should end up with the correct structure.”
What part of folding structure are disulfide bonds considered?
“The disulfide bridge is not a great example of 3° structure because it is a covalent bond, not a hydrophobic interaction. However, because the disulfide is formed after 2° structure and before 4° structure, it is usually considered part of 3° folding.
“Which of the following may be considered an example of tertiary protein structure?
I.van der Waals interactions between two Phe R-groups located far apart on a polypeptide
II.Hydrogen bonds between backbone amino and carboxyl groups
III.Covalent disulfide bonds between cysteine residues located far apart on a polypeptide”
I and III
What are the forces involved in stabilizing quaternary structure
“The forces stabilizing quaternary structure are generally the same as those involved in secondary and tertiary structure—non-covalent interactions (the hydrogen bond, and the van der Waals interaction). But also covalent Disulfide bonds! Like antibodies or insulin
“What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?”
“ Quaternary disulfides are bonds that form between chains that aren’t linked by peptide bonds. Tertiary disulfides are bonds that form between residues in the same polypeptide.”
“The hydrolysis of polysaccharides into monosaccharides is ______ thermodynamically.”
Favored
“However, this hydrolysis does not occur at a significant rate without enzymatic catalysis.”
“Humans are mammals, so how can we digest lactose, which has a β linkage?
we have a specific enzyme, lactase, which can digest lactose. This is an exception to the rule that mammalian enzymes cannot hydrolyze β-glycosidic linkages.”
“If the activation energy of polysaccharide hydrolysis were so low that no enzyme was required for the reaction to occur, would this make polysaccharides better for energy storage? ”
“No, because then polysaccharides would hydrolyze spontaneously (they’d be unstable). The high activation energy of polysaccharide hydrolysis allows us to use enzymes as gatekeepers—when we need energy from glucose, we open the gate of glycogen hydrolysis.”
“Fatty acids are composed of long unsubstituted alkanes that end in a carboxylic acid. The chain is typically 14 to 18 carbons long, and because they are synthesized two carbons at a time from acetate, only _____ fatty acids are made in human cells.”
even-numbered
“Unsaturated fatty acids have one or more double bonds in the tail. These double bonds are almost always _______
(Z) (or cis).”
The hydrophobic interaction results from the fact that water molecules must form an orderly solvation shell around each hydrophobic substance. ”The problem is that forming a solvation shell is what related to thermodynamics and entropy?
increase in order and thus a decrease in entropy (∆S
“ Fats are more efficient energy storage molecules than carbohydrates for what two reasons:
packing and energy content.”
“Packing: Their hydrophobicity allows fats to pack together much more closely than carbohydrates. Carbohydrates carry a great amount of water-of-salvation
“a fat has more energy carbon-for-carbon than a carbohydrate. The reason is that fats are much more reduced.”
“Since carbohydrates are more oxidized to start with, oxidizing them releases less energy.”
“Phospholipids are _______, substances that efficiently solubilize oils while remaining highly water-soluble.
detergents;
Detergents are like soaps, but stronger.”
“Would a saturated or an unsaturated fatty acid residue have more van der Waals interactions with neighboring alkyl chains in a bilayer membrane?”
“The bent shape of the unsaturated fatty acid means that it doesn’t fit in as well and has less contact with neighboring groups to form van der Waals interactions. Phospholipids composed of saturated fatty acids make the membrane more solid.”
“A more precise way to give the answer to the question above is to say that double bonds (unsaturation) in phospholipid fatty acids tend to increase membrane fluidity.”
