Dawn - BIO - Flashcards
How are Vmax and Km affected with a competitive inhibitor?
For Competitive inhibition the Vmax does not change, and the Km increases
What is secondary active transport and how does it differ from primary active transport?
Secondary active transport requires the input of energy to transport molecules across a membrane, BUT it does not have direct coupling of ATP (seen in primary active transport).
How does an uncompetitive inhibitor work? and what are the ideal conditions?
Uncompetitive inhibitors cannot act until the Enzyme and substrate bind together, thus, it works best when substrate concentration is high. (note: this causes Km and Vmax to decrease, meaning that the enzymes apparent affinity for the substrate increases and the maximum enzyme activity decreases)
What does a hill coefficient of 2.8 mean?
A hill coefficient greater than 1 = positive cooperativity (binding at one position or active site = occurs more easily). This creates a sigmoidal graph not a linear graph. Meaning that the second substrate molecule binds significantly more readily than its first
What is difference between cofactor, coenzyme, prosthetic group and apoenzyme
- Metal ions = cofactors (inorganic)
- Coezyme = organic cofactors
- Prosthetic group = cofactors that are tightly bonded to their enzymes
- Apoenzyme = Enzyme without its required cofactors
What is the difference between phosphatases and kinases?
- Phosphotases remove phosphate groups
- Kinases add phosphate groups (phosphorylation)
What pathways uses allosteric enzymes the most?
Feedback loops
Which amino acids are most likely to become phosphorlyated?
- Kinases phosphorylate the substrate!
- Most likely to be phosphorylated if they have -OH group attached (STY)
If the oxidation of NAD is blocked what happens to the NADH/NAD+ ratio?
The ratio will increase because the NADH cannot be oxidized to NAD+
How many carbons do oxaloacetate, acetyl-CoA, Ribose, and g-3-p have?
- Oxaloacetate = 4C
- Acetyl CoA = 2
- Ribose = 4
- g-3-p = 6
What is the greatest contributor to the change in free energy associated with protein folding?
- Change in DeltaS (entropy) because you want a large negative number to get a large negative deltaG
- Primary driving force behind protein folding is increased entropy made possible by the sequestration of hydrophobic residues in the protein core (make a tight, ordered cage = entropically unfavorable)
What would most likely increase glycolytic enzyme activity via allosteric regulation?
- Upregulation of glycolytic activity
- Increase [AMP] and low [ATP]
What does it mean for an amino acid to be ketogenic?
- Ketogenic amino acids that yield acetyl-
CoA or acetoacetyl-CoA - Meaning they do NOT produce intermediates that can be converted to glucose
- Lysine
(K) and Leucine (L) are the only amino acids that are exclusively ketogenic.
What is the best explanation for the finding that the substitution of pro residues on a protein can cause up to a
75% decrease in alpha helix formation compared with the native protein?
The ring on proline causes too much strain to be bent sufficiently in the helix.
- Proline is the only amino
acid whose amine group forms a ring. This means that it is unable to twist and turn with the same fluidity as
other amino acids.
What does it mean for an amino acid to be glucogenic?
- Glucogenic amino acids are amino acids which, when metabolized, yield pyruvate or Krebs cycle
intermediates, or that can be converted to glucose through gluconeogenesis. - They are alanine (A), arginine (R),
asparagine (N), aspartate (D), cysteine (C), glutamic acid (E), glycine (G), histidine (H), valine (V), methionine
(M), proline (P), and serine (S).
How many turns per residue are there for an alpha and a pi helix?
- Alpha - every 4th AA (3.6) with 5.4 angstroms between
2. Pi - every 5th (4.1)
A dipeptide is formed through the reaction of one
amino acid with another to form a peptide bond.
During this reaction, the nucleophile is:
- The amino terminal nitrogen of one of the
amino acids. - Peptide
bonds form between the amino terminal of one
amino acid and the carboxylic acid terminal of
another - They do not directly involve side chains
and the amino terminal nitrogen of one amino acid attacks the carbonyl carbon
of another.
The pKa of the side chain of histidine is
approximately 6. In a solution with a pH of 8, the
side chain of histidine is most likely to be:
Since the
side chain of histidine contains an N-H (which
is specifically part of an imidazole ring), it will
be positively charged when it is protonated and
uncharged when it is deprotonated.
How do you calculate the PI of histidine?
calculate isoelectric point, you
must consider the pKa values of the amino acid in
question. Histidine has a carboxylic acid group
(pKa ~ 2), an amino group (pKa ~ 9), and its side
chain (pKa ~ 6). Note that we should not average all
three of these values; instead, since histidine is a
basic amino acid, we should average the two most
basic pKas. (6 + 9) / 2 = 7.5.
What are the steps to Gabriel malonic ester synthesis?
- malonic ester
with a good leaving group (usually a halide, such as Br) attached to the alpha carbon - An SN2 reaction then takes
place with a nitrogen that is very carefully protected in the form of a bicyclic compound known as phthalimide. - The –H at the alpha-carbon is slightly acidic, so treatment with a strong base will deprotonate and allow R–X (where R is the side group of the
amino acid we’re interested in synthesizing and X is usually a halide) to attach to the alpha carbon. - Remove substituents
- Hydrolysis under basic
or acidic conditions will remove the phthalamide ring and convert the ester (COOR) groups to carboxylic acids
(COOH) - one round of decarboxylation through heat will remove the surplus COOH group, leaving us
with our amino acid.
What values of Kcat and Km do you need to have to display high specificity?
High Kcat, and low Km bc = Kcat/Km
What is the primary difference between microtubules and actin filaments?
Only actin filaments are capable of branched assembly, microtubule assembly can only produce single, straight microtubules, without branch points
If researchers wished to determine if myosin were necessary for proper cell function, which motility function
should be monitored in the experiment?
- Cleavage furrow formation in hepatocytes
- which aids the process of cytokinesis (daughter cell separation at the end of cell division), is based on the contraction of an array of actin filaments that are anchored to the plasma membrane
- The sliding of actin filaments is induced by the action of the motor protein myosin, which splits the parent cell into 2 daughter cells.
What is composed of actin?
- Microfilaments, not microtubules