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mid 2 Flashcards

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1
Q

How do enzymes function?

A

By lowering the activation energy needed for a reaction

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2
Q

Enzyme

A

In Michaelis-Menten kinetics, the substrate concentration at which the reaction rate is half of Vmax is called KM

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3
Q

First Order:

A

Reaction rate depends on the concentration of one reactant

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4
Q

Second Order:

A

Reaction rate depends on the concentration of two reactants

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5
Q

Pseudo-first Order:

A

Two-reactant reaction where one reactant is present in large excess

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6
Q

In a Lineweaver-Burke plot (1/V0 vs. 1/[S]), where can you find Vmax?

A

It is the reciprocal of intercept on the y-axis

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7
Q

In noncompetitive inhibition, what happens to Vmax and KM?

A

Vmax decreases but KM remains the same because inhibitor binding is independent of substrate binding.

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8
Q

Uncompetitive inhibitor

A

Binds only to the enzyme-substrate complex, preventing the reaction from proceeding to product.

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9
Q

An inhibitor that binds to a site other than the active site and cannot be overcome by increasing substrate concentration is called a …

A

Noncompetitive inhibitor.

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10
Q

Competitive inhibition ______ the apparent KM of the enzyme. (Increases, decreases, remains)

A

Increases

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11
Q

Which amino acids make up the catalytic triad in chymotrypsin?

A

Aspartate 102, Histidine 57, and Serine 195. These residues come together to form the active site when the protein folds

Asp 102: This residue forms hydrogen bonds with His 57 to help fix the geometry

His 57: acts a general base and abstracts a proton from Ser 195

Ser 195: ionized by His 57 and becomes a very strong nucleophile

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12
Q

In chymotrypsin catalysis, what role does serine play?

A

It acts as a nucleophile attacking the peptide bond.

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13
Q

Which of the following is a model for allosteric regulation?

A

Concerted model

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14
Q

An allosteric activator ______ substrate binding. (Increases, decreases, remain)

A

Increase

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15
Q

In the concerted model, the T state is:

A

Low-affinity, inactive state

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16
Q

Myoglobin shows cooperative oxygen binding. (True/false)

A

False

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17
Q

Fetal hemoglobin has _____ affinity than adult. (Higer, lower, same)

A

Higher

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18
Q

Allosteric regulation always increases enzyme activity. (True, false)

A

False

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19
Q

Myoglobin

A

Myoglobin is a monomer (single subunit) and lacks the quaternary structure necessary for allosteric regulation and cooperative binding

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20
Q

Epimers are a type of diastereoisomer. (True, false)

A

True

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21
Q

D-glucose and D-mannose are epimers. (True, false)

A

True

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22
Q

D-glucose and D-mannose are stereoisomers. (True, false)

A

True

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23
Q

Cellulose is composed of:

A

β-1,4 glycosidic bonds

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24
Q

Humans can digest both starch and cellulose. (True, false)

A

False

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25
Michaelis-Menten kinetics
The substrate concentration at which the reaction rate is half of Vmax is called KM
26
What is the role of DNA helicase during DNA replication?
Unwinds the DNA double helix
27
The double helix structure of DNA is stabilized primarily by:
Hydrogen bonds and base stacking interactions
28
DNA replication is semi-conservative, meaning each new double helix consists of one parental and one newly synthesized strand. (True, false)
True
29
DNA polymerase
Adds nucleotides to a growing DNA strand
30
Primase
Lays down an RNA primer
31
DNA ligase
Seals nicks between Okazaki fragments
32
DNA helicase
Unwinds the DNA double helix
33
Cellulose differs from amylose in that:
It has β-1,4 glycosidic linkages
34
Which lipid is a precursor for steroid hormones?
Cholesterol
35
Which glycosidic linkage is found in amylose?
α-1,4
36
Okazaki fragments are found on the leading strand. (True, false)
False
37
Peripheral membrane proteins cross the hydrophobic core of the lipid bilayer. (True, false)
False
38
Which of the following lipids has a structure composed of four fused carbon rings?
Cholesterol
39
Which membrane component is primarily responsible for selective permeability?
Integral membrane proteins
40
Primase synthesizes short RNA primers to provide a starting point for DNA synthesis. (True, false)
True
41
A reaction whose rate is directly proportional to the concentrations of two reactants is a _______ reaction.
Second order
42
At _____, the forward and reverse reactions occur at the same rate, resulting in no net change in the concentrations of products and reactants.
Equilibrium
43
The ration kcat/Km is known as the _____ and is used to compare enzyme performance under low substrate conditions.
Catalytic efficiency
44
_____ enzymes display sigmoidal kinetics and are regulated by effectors that bind sites other than the active site.
Allosteric
45
The velocity at the beginning of a reaction is called ___
Vo
46
What is the biochemical advantage of having a KM approximately equal to the substrate concentration normally available to an enzyme?
The enzyme operates at about half its maximum velocity (1/2 vmax) when the substrate concentrations is approximately equal to KM. This makes the enzyme sensitive to changes in substrate concentration, allowing for efficient regulation of enzyme activity under physiological conditions.
47
Describe the molecular mechanism of oxygen binding to one subunit of hemoglobin and how this interaction induces coopperative binding throughout the molecule.
When oxygen binds to one subunit of hemoglobin, it binds the iron ion and pulls it into the heme plane, pulling on a histidine part of a α-helix. This causes the helix to shift, changing the shape of the whole protein (T state to R state). This structural change increases the oxygen-binding affinity of the other subunits, allowing cooperative binding.
48
Number 4 on Assignment 3
49
O2 (regulator of hemoglobin)
(i) homotropic regulator (ii) Binds to the Fe2+ in the heme, pulling it into the plane of the ring. This shifts hemoglobin from the T state to the R state, increasing affinity in other subunits & cooperative binding.
50
CO2 (regulator of hemoglobin)
(i) heterotropi regulator (ii) Reacts with N-terminal amino groups to from carbamates, which stabilize the T state. This lowers hemoglobin's O2 affinity and promotes O2 release in tissues.
51
H+ (regulator of hemoglobin)
(i) heterotropic regulator (ii) Protonation of His146 allows a salt bridge to form with Asp94, stabilizing the T state and promoting O2 release.
52
Number 6 on Assignment 3
53
Number 7 on Assignment 3
54
Determining Michaelis vs Allosteric
Compare V0. Michaelis shows a hyperbolic curve that levels out when reaching Vmax. Allosteric exihibit a sigmoidal response showing a rapid increase of V0 at threshold.
55
Covalent Catalysis
This strategy involves the active site side chains transiently forming a covalent interaction with the substrate
56
Acid-Base Catalysis
This involves an amino acid side chain donating or accepting a proton that is needed for a reaction
57
Metal-ion catalysis:
This strategy is used by metalloenzymes. These metal ions help to stabilize a negative charge in a transition state due to their positive charge
58
Catalysis by approximation
involves the enzyme bringing substrates into proximity and in the correct orientation relative to each other to facilitate a reaction
59
Concerted Model
1. enzyme must have a quaternary structure, consisting of multiple subunits 2. a tense state (T state) which is inactive and cannot bind substrate (represented as squares), and a relaxed state (R state) which is active and can bind substrate (represented as circles
60
Oxyanion hole
stabilizes the transition state, interacts with the negatively charged oxygen that appears in the transition state of peptide bond cleavage
61
Specificity Pocket (Substrate binding pocket)
interacts with the substrate and influences which molecules can bind. In chymotrypsin, this pocket is lined with hydrophobic residues and promotes the binding of hydrophobic substrates
62
Regulators (Allosteric)
Activators: Stabilize the R state, shifting the sigmoidal curve to the left (less substrate needed for the same response) Inhibitors: Stabilize the T state, shifting the curve to the right (more substrate needed for the same response)
63
Homotropic Regulator
A regulator where the substrate itself is the regulatory molecule
64
Heterotropic Regulator
A regulator that is a molecule other than the substrate for the enzyme, such as a metabolite in a pathway
65
Enzyme Inhibition
The process where drugs or environmental toxins bind to enzymes and make them not work
66
Reversible Inhibition
Inhibitors that can bind and come off the enzyme
67
Irreversible Inhibition
Inhibitors that typically covalently bind to the enzyme or bind very tightly
68
Competitive Inhibition
1. competitive inhibitor binds to active site of enzyme - **Increase in KM** to reach 1/2Vmax = increase in [S] - **Vmax = unchanged** - Inhibition by a competitive inhibitor **can be overcome by increasing the substrate concentration**
69
Noncompetitve
2. non-competitive inhibitor binds to a site other than the active site - **KM remains unchanged** - **Vmax decreases** - adding more substrate **cannot overcome the inhibition** caused by a non-competitive inhibitor
70
Uncompetitive
3. uncompetitive inhibitor binds only to the enzyme-substrate complex, preventing the reaction from proceeding to product. - require the enzyme to first bind to its substrate, forming the **enzyme-substrate complex (E-S complex)**, before the inhibitor can bind - **KM decreases** - **Vmax decreases** - adding more substrate **does not help overcome this type of inhibition**
71
Best to Worst for humans
Cis unsaturated > Saturated > Trans unsaturated
72
Lipid Bilayer
hydrophilic head groups facing outwards and hydrophobic tails facing inwards
73
Integral Membrane Proteins:
Proteins that are embedded in or span the lipid bilayer
74
Peripheral Membrane Proteins
Proteins that are attached to the surface of the membrane (via a lipid anchor or interaction with another membrane protein) but are not embedded in the bilayer

biochem mid 2 (1 decks)

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