Biochem Flashcards
What is the 3-letter code for arginine?
Arg.
What is the structure of histidine?
Which amino acid is Pro?
Proline.
Which amino acid is Y?
Tyrosine.
Which amino acid is Leu?
Leucine.
Which amino acid is this?
Asparagine.
What 3 major properties of metal ions make them good enzymatic cofactors?
Increased reactivity due to…
- Positive charge
- Ability to form strong, but kinetically labile bonds
- Can be stable in more than one oxidation state
Which amino acid is this?
Glutamine.
Which amino acid is Q?
Glutamate.
What is the typical pKa of an amino acid’s terminal α-carboxyl group?
3.1
What is the MM equation?
An equation describing hyperbolic enzyme activity.
Define endergonic reaction.
A reaction that is energetically unfavourable (positive ΔG), and will require an input of energy (not spontaneous).
What is the 3-letter code for leucine?
Leu.
What is a carboxamide?
Which amino acid is D?
Aspartic acid.
Which amino acid is A?
Alanine.
Which amino acid is Phe?
Phenylalanine.
Which amino acid is C?
Cysteine.
Which 2 amino acids are negatively charged?
Aspartic acid (Asp) and glutamic acid (Glu).
What is the typical pKa of aspartic and glutamic acid?
4.1
How are glutamine (Gln) and asparagine (Asn) structurally related?
Both have terminal carboxamide (-C=ONH2) groups in their side chains, but Gln’s side chain is one CH2 group longer than Asn’s.
Which amino acid is this?
Proline.
Which amino acid is this?
Tyrosine.
What is the structure of aspartic acid?
What is the 1-letter code for alanine?
A.
Which amino acid is Glu?
Glutamic acid.
Which amino acid is Gln?
Glutamate.
In enzyme kinematics, what does KM represent?
The likelihood that the enzyme’s active site is populated with substrate: (rate of product breakdown) ÷ (rate of product formation).
How are phenylalanine (Phe) and tyrosine (Tyr) structurally related?
Both have terminal aromatic rings attached to the β-C, but Tyr has a hydroxyl (-OH) group making it a phenol rather than a benzene ring.
In enzyme kinematics, what is true of KM when the reaction is at half of its maximum velocity?
KM is equal to substrate concentration.
What is the 3-letter code for tyrosine?
Tyr.
What is the 3-letter code for threonine?
Thr.
Which amino acid is especially sensitive to changes in physiological pH?
Histidine (pKa 6.0).
What is the structure of cysteine?
Which amino acid is this?
Leucine.
Which amino acid is L?
Leucine.
What is the 3-letter code for aspartic acid?
Asp.
What is an indole?
What is the 3-letter code for glutamine?
Gln.
What is the key difference between enzymatic cofactors and substrates?
Substrates are highly specific to individual enzymes, but cofactors are not - many enzymes may use the same cofactor.
What is the 3-letter code for tryptophan?
Trp.
Which amino acid is this?
Tryptophan.
What is the typical pKa of tyrosine?
10.9
Which amino acid is this?
Alanine.
What are the 3 major physiological roles of carbonic anhydrase?
- Dehydrate HCO3- in the blood to form CO2 for exhalation
- Convert CO2 to bicarbonate for aqueous humor of the eye
- Coupling with other enzymatic processes to speed them up even more
What is the 1-letter code for cysteine?
C.
Which amino acid is this?
Serine.
What does it mean if ΔG = 0?
The system is at equilibrium, and no net change can take place.
What is the 3-letter code for glycine?
Gly.
What does ΔG represent in a reaction?
The free-energy change of a reaction; the reaction will only take place spontaneously if ΔG is negative (exergonic), and will require an energy input if ΔG is positive (endergonic).
Which amino acid is R?
Arginine.
Which amino acid is this?
Arginine.
Define prosthetic group.
A tightly bound cofactor required for a protein’s activity.
What is the 1-letter code for phenylalanine?
F.
What is the 1-letter code for tryptophan?
W.
What is the structure of arginine?
Which amino acid is Tyr?
Tyrosine.
What is the 1-letter code for isoleucine?
I.
What is the structure of glycine?
Which amino acid has an indole group as part of its side chain?
Tryptophan (Trp).
What is the structure of alanine?
Which amino acid is Gly?
Glycine.
What is the typical pKa of lysine?
10.8
What is chymotrypsin?
A moderately selective digestive enzyme that cleaves peptide bonds after bulky aromatic residues.
How does the partial double-bond character of peptide bonds make them resistant to hydrolysis?
- Strengthens the C-N bond
- Stabilizes the carbonyl C, making it less susceptible to nucleophilic attack
Which is the most basic amino acid?
Arginine (pKa 12.5).
What is the 1-letter code for histidine?
H.
Which 6 amino acids are polar, but uncharged?
- Serine
- Threonine
- Tyrosine
- Asparagine
- Glutamine
- Cysteine
Which amino acid is involved in disulfide bonds? How?
Cysteine: 2 Cys residues undergo an oxidation reaction (losing H2) to link the S atoms of their thiol (-SH) groups.
Which amino acid is this?
Histidine.
Which amino acid is Ser?
Serine.
Which amino acid is this?
Threonine.
What is a thioether?
What is the 1-letter code for glutamine?
Q.
Define exergonic reaction.
A reaction that is energetically favourable (negative ΔG) and will take place spontaneously.
What is the 3-letter code for histidine?
His.
Which amino acid is W?
Tryptophan.
What is the 3-letter code for asparagine?
Asn.
What is the 1-letter code for asparagine?
N.
What is the typical pKa of histidine?
6.0
Why is the peptide bond essentially planar?
Resonance gives the bond between the C terminus of the first residue and the N terminus of the next a partial double-bond character, preventing rotation about the bond.
Which amino acid is G?
Glycine.
What is the most common cis peptide bond? Why?
X-Pro: the cyclic structure of proline means both trans and cis conformations are equally sterically hindered, so there is no preference for one or the other.
Which amino acid is Asp?
Aspartic acid.
What does it mean when an enzymatic reaction yields a sigmoidal plot (rather than hyperbolic)?
There is a lag phase: substrate binding to enzyme doesn’t result in immediate performance, as the enzyme (allosteric) is converted to a more productive system first.
What is the 3-letter code for isoleucine?
Ile.
What is the typical pKa of cysteine?
8.3
What is the 1-letter code for arginine?
R.
Which amino acid is Cys?
Cysteine.
Which amino acid is Arg?
Arginine.
Which amino acid is E?
Glutamic acid.
Which amino acid is this?
Aspartic acid.
Which amino acid is N?
Asparagine.
What is the structure of leucine?
How are serine (Ser) and threonine (Thr) structurally related?
Both have a terminal hydroxyl (-OH) group on their β-C, but Thr has an additional CH2 group on the β-C.
What is imidazole?
Which amino acid is this?
Valine.
What is the 1-letter code for tyrosine?
Y.
What is the structure of tryptophan?
What is the 1-letter code for glutamic acid?
E.
What is the structure of glutamine?
Which amino acid is this?
Lysine.
Which amino acid is F?
Phenylalanine.
What makes histidine (His) different from arginine (Arg) and lysine (Lys)?
All 3 are positively charged, but Arg and Lys have aliphatic side chains, while His has an aromatic side chain.
What is the 1-letter code for threonine?
T.
Which amino acid is Ile?
Isoleucine.
Which amino acid is Asn?
Asparagine.
What is the typical pKa of arginine?
12.5
Which amino acid is I?
Isoleucine.
What is the structure of tyrosine?
Which amino acid contains a thioether group in its side chain?
Methionine (Met).
What is the structure of glutamic acid?
In enzyme kinematics, what does a low KM value signify?
Product is highly likely to form.
What is the 3-letter code for glutamic acid?
Glu.
Which amino acid is H?
Histidine.
What is the structure of phenylalanine?
In enzyme kinematics, what does a high KM signify?
Product is unlikely to form.
What was the first enzyme to be identified as containing zinc?
Carbonic anhydrase.
Which amino acid is this?
Methionine.
Which key component is essential to the catalytic activity of carbonic anhydrase?
A bound zinc ion (Zn2+).
Which 2 amino acids have a terminal carboxamide as part of their side chains?
Asparagine (Asn) and glutamine (Gln).
Which amino acid is this?
Phenylalanine.
Define apoenzyme.
A cofactor-dependent enzyme that does not have its cofactor and is therefore catalytically inactive.
What is the difference between ΔG and ΔG‡?
ΔG is the free energy difference between products and reactants, and ΔG‡ is the free energy required to form the transition state; the two are generally unrelated. ΔG‡ determines the rate of the reaction, while ΔG provides no information about reaction rate.
What is the structure of methionine?
What is the 3-letter code for lysine?
Lys.
Define Gibbs free energy.
A thermodynamic property that measures the amount of energy capable of doing work.
What is the 3-letter code for phenylalanine?
Phe.
What is the structure of asparagine?
How is ΔG determined?
The free energy of the products (final state), minus the free energy of the reactants (initial state).
Which secondary structure is more common in proteins: left-handed or right-handed α-helices? Why?
Right-handed: they are energetically more favourable because there is less steric clash between side chains and the backbone.
What is the 1-letter code for lysine?
K.
Which amino acid is S?
Serine.
Which amino acid is this?
Glycine.
What is the structure of lysine?
What is the 3-letter code for alanine?
Ala.
What is the structure of proline?
What is the 1-letter code for glycine?
G.
Define holoenzyme.
A cofactor-dependent enzyme that has its cofactor and is thus complete and catalytically active.
Which amino acid is M?
Methionine.
Which 3 amino acids are positively charged?
Lysine (Lys), arginine (Arg), and histidine (His).
What is papain?
An enzyme (found in papaya plants) that catalyzes the cleavage of any peptide bond.
Which amino acid is His?
Histidine.
What makes aspartic acid (Asp) and glutamic acid (Glu) different from asparagine (Asn) and glutamine (Gln)?
Asp and Glu are derivatives of Asn and Gln, respectively, with terminal carboxylic acid groups instead of carboxamide groups on their side chains (rendering them negatively charged).
What is trypsin?
An enzyme that catalyzes the cleavage of peptide bonds only on the carboxyl side of lysine (Lys) and arginine (Arg) residues.
What is the 1-letter code for serine?
S.
What is the 1-letter code for aspartic acid?
D.
What is the 1-letter code for proline?
P.
Which amino acid has an imidazole group as part of its side chain?
Histidine (His).
What is the 3-letter code for proline?
Pro.
What is the structure of serine?
Do most peptide bonds show a preference for trans or cis conformation? Why?
Most prefer trans due to steric clashes between α-C-attached groups in cis conformations.
Which amino acid is V?
Valine.
What is the typical pKa of an amino acid’s terminal α-amino group?
8.0
What is the structure of isoleucine?
What is the 3-letter code for serine?
Ser.
What is the 1-letter code for methionine?
M.
Which amino acid is Met?
Methionine.
Which amino acid is Val?
Valine.
What is the 3-letter code for cysteine?
Cys.
Which amino acid is Trp?
Tryptophan.
Which amino acid is K?
Lysine.
How many CH2 groups are there between the β-carbon and the terminal functional group of the side chains of arginine (Arg) and lysine (Lys)?
2 (not including the β-C).
Which amino acid is Lys?
Lysine.
What does ΔG‡ represent?
Free energy of activation, i.e. the energy required to form the transition state from the substrate of a reaction.
What is the function of the bound Zn2+ ion in carbonic anhydrase?
A water molecule binding to Zn2+ has its pKa lowered from 15.7 to 7, which means it will deprotonate at pH 7 to form Zn-bound OH-. This OH- is a potent nucleophile and will attack CO2 much more readily than water does.
Which amino acid has a guanidium group as part of its side chain?
Arginine (Arg).
What is the 1-letter code for leucine?
L.
What is the 3-letter code for valine?
Val.
What is thrombin?
An enzyme involved in blood-clotting that catalyzes the cleavage of peptide bonds between Arg and Gly in specific sequences only.
Which amino acid is Thr?
Threonine.
Define free energy of activation.
The energy required to form the transition state from the substrate of a reaction.
Which amino acid is this?
Isoleucine.
In enzyme kinematics, what does Kcat represent?
Catalytic rate constant: the number of substrate molecules converted to product in a given amount of time when an enzyme is fully saturated, i.e. how fast the reaction can go at full throttle.
What is the structure of threonine?
What is the major end product of aerobic respiration?
CO2.
What is guanidium?
What is the 1-letter code for valine?
V.
Which amino acid is this?
Cysteine.
What is the structure of valine?
Which amino acid is this?
Glutamic acid.
Which amino acid is T?
Threonine.
What is the 3-letter code for methionine?
Met.
Which amino acid is Ala?
Alanine.
Which amino acid is P?
Proline.
If peptide bond hydrolysis is thermodynamically favourable, why does it require a catalyst?
Without a catalyst, it’s too slow (10-1000 years!!); the double-bond character makes the carbonyl C resistant to nucleophilic attack, so an enzyme is needed to make it more susceptible to hydrolysis.
What is the key reactive component of chymotrypsin?
Ser 195, an especially reactive Ser residue (1 of 28 possible Ser residues on the enzyme).
Define binding energy (catalysis).
The free energy released in the formation of a large number of weak interactions between enzyme and substrate.
What are the 2 major impacts of binding energy on enzyme catalysis mechanisms?
- Substrate specificity: only the right substrate has the right # of interactions to yield the right amount of binding energy
- Catalytic efficiency: the full complement of interactions only forms when the ES complex is in transition state
What is the catalytic triad of chymotrypsin?
Serine, histidine, and aspartate.
What structural element of chymotrypsin determines its substrate specificity?
The hydrophobic S1 pocket: it binds large nonpolar residues to position adjacent peptide bonds for cleavage, so specificity depends on which amino acid is on the N-terminal side of the bond to be cleaved.
Define scissile bond.
A bond to be cleaved, e.g. by a proteolytic enzyme.
What is the key structural difference between chymotrypsin and trypsin affecting specificity?
Trypsin has an Asp instead of a Ser in the bottom of its S1 pocket, so it attracts and stabilizes positively charged substrate side chains (Arg and Lys).
What is the key structural difference between chymotrypsin and elastase affecting specificity?
Elastase has 2 Val residues replacing smaller residues near the top of the S1 pocket, blocking off the mouth of the pocket so that only small side chains (e.g. Ala, Ser) can enter.
How does the binding of a water molecule to the zinc ion in carbonic anhydrase favour formation of the transition state?
- Facilitates H+ release to make a stronger nucleophile (OH-)
- Positions the Zn-bound water molecule in close proximity to bound CO2 substrate (on nearby hydrophobic patch)
