Unit 2 - Active Recall Flashcards
What does catalysis do?
- lowers the activation energy for a reaction
- increase reaction rates by decreasing ΔG ‡
- A lower ΔG ‡ allows more molecules to react
What is the ‘reaction coordinate’ equation?
ΔG° = ΔH° – TΔS° = -RTlnKeq
How do you increase rxn rates?
Increasing number of molecules, increasing the temperature, or adding a catalyst will increase reaction rates
List all that you know about protein catalysts (enzymes)?
Note: riboenzymes not included
- Are the largest group of proteins (six families)
- Have active sites that bind substrate/product
- Put substrates in proximity, with correct orientation and provide functional groups for catalysis (decrease activation energy)
- Preferentially bind and stabilize the transition state (induced fit)
- Do not change the reaction equilibrium (i.e. catalyze reaction in both directions)
- Are not chemically changed by the reaction
- Are normally present in low amounts relative
to the reactants and products - have characteristic pH and temperature optima
Enzymes typically increase reaction rates by ___________ fold. And _________ fold maximally.
10^8 – 10^12 fold
max of 10^17 fold
What do enzymes stabilize?
The enzyme stabilizes the transition state
Enzymes use three types of catalysis. Explain each.
- Acid-base catalysis: transfer or removal of H+
- Covalent catalysis: transient formation of a covalent bond between enzyme and substrate
- Metal catalysis: direct or indirect role in catalysis; often oxidation-reduction Rx
Describe how chymotrypsin uses a catalytic triad to
hydrolyze a peptide bond.
- Chymotrypsin uses both covalent and acid-base catalysis to hydrolyze a peptide bond (enhancement of ~ 1010)
- Triad used: Asp 102, His 57, Ser 195
Explain the chymotrypsin mechanism step by step.
- His accepts a proton from Ser (base catalysis) allowing the nucleophilic oxygen of serine to attack the carbonyl carbon of the substrate (covalent catalysis)
- His donates a proton to the new NH2 of the C-terminal peptide fragment, breaking the peptide bond (Tetrahedral intermediate transition state)
- Departure of the Rc leaves the enzyme covalently
bound to the RN region of the substrate (Acyl-enzyme intermediate - stable & covalent) - Water donates a proton to His 57 and resulting OH- attacks the carbonyl group of substrate (resembles step 1)
- His 57 donating a proton leads to collapse of the
second tetrahedral intermediate (resembles step 2) - N-terminal portion of substrate diffuses away,
regenerating chymotrypsin
What other information do you recall about chymotrypsin catalysis?
- Even with mutation of Asp 102, His 57, and Ser 195, proximity and orientation still enhance the reaction rate by 10^5
- Mutants with Ser 195 replaced are at least 106 fold less active
- Mutants with Asp 102 or His 57 replaced are 1,000 fold less active
- Gly 193 and a backbone amide stabilizes the transition state
Explain chymotrypsin substrate binding pocket?
- substrate binding pocket complements the substrate
- lets us know that divergent evolution of chymotrypsin has occurred
Note:
- Catalytic triads are used throughout biology
What is the Michaelis-Menten Equation?
V = Vmax[𝑆] / 𝐾m + [𝑆]
note:
-hyperbolic (like hemoglobin)
What is the catalytic rate constant (kcat ) and its equation?
kcat = Vmax / [E]total
note:
- kcat = catalytic rate constant or turnover number, when the enzyme is saturated with S (substrate)
- determines how quickly an enzyme can act
Lineweaver-Burk plot linearizes Michaelis-
Menten kinetics data..give the equation.
1/V = (Km / Vmax) (1/[S]) + (1/Vmax)
note:
- very similar to y=mx+b
- Vmax and KM are the two most important parameters for an enzyme, and are easy to estimate with a Lineweaver-Burk plot
Give an example of an irreversible enzyme inhibition (ie: irreversible inhibitors)
Diisopropylfluorophosphate is an irreversible inhibitor of chymotrypsin
Exceptions to Michaelis-Menten kinetics
- Michaelis-Menten kinetics are only valid for the simplest enzyme reactions
- Many enzymes require multiple substrates/products and/or require multiple steps
- For multistep reactions KM is a complicated function of many rate constants
Explain role of allosteric enzymes & effectors
- Allosteric (”other site”) enzymes often have multiple subunits and show cooperativity: (analogous to hemoglobin vs myoglobin)
- Enzymes can have positive or negative allostery
- Allosteric (“other site”) effectors may inhibit or activate enzymes and are used to control metabolic pathways
What do you know about lipids?
- Lipids are heterogeneous, hydrophobic (or amphipathic), and thus insoluble
- Lipids associate into larger structures and are not usually free in solution (due to hydrophobic effect)
- Due to potential to aggregate, lipid storage and transport is a challenge
- Cellular structures (membrane bilayers,
vesicles) - Energy storage (fat = triacylglycerols)
- Bioactivity (messengers, vitamins, hormones)
List types of lipids
- Fatty acids (FAs: aliphatic carboxylic acids)
- Triacylglycerols (TAGs: 3 FAs esterified to
glycerol) - Phospholipids (PLs: phospho-head group attached to diacylglycerol or ceramide)
- Isoprenoids/steroids (e.g. cholesterol)
Glycolipids (glycosphingolipids)
What do you know about fatty acids?
- are amphipathic (hydrophilic carboxyl group and hydrophobic hydrocarbon tail of variable length)
- FAs may be saturated (no double bonds), mono- or poly-unsaturated
- Most natural unsaturated FAs have unconjugated cis double bonds (“trans” fats mainly derived artificially)
- may be saturated (no double bonds), mono- or poly-unsaturated
- most FAs are found esterified to cholesterol (CE) or to
glycerol (TAGs or PLs), or are bound to albumin in the blood
What are the two types of nomenclature for FA double bonds?
- Omega nomenclature: Count the carbons starting from the tail to the first double bond (the tail carbon is always referred to as the ω (omega) carbon, while that next to the carboxy carbon is α)
- ex: 18:3(n-3) or 18:3ω-3 - delta nomenclature: Count the carbons starting from the carboxyl group: list positions of the double bonds (assume cis unless otherwise specified)
- 18:3(9,12,15) or 18:3Δ 9,12,15
What do you know about triacylglycerols?
- TAGs (also called triglycerides) consist of 3 FAs esterified to glycerol: they are found in circulating lipoproteins or in insoluble cytosolic lipid droplets
- In adipose tissue, stored TAG in droplets can be hydrolyzed to release FFA and glycerol for delivery to
the liver and other tissues - TAGs are the major energy reserve in the body: oxidation of FAs produce over twice the energy per gram compared to carbohydrates
What do you know about glycerophospholipids?
- Most phospholipids (PLs) are esters of 3- glycerophosphate, two FAs, and a polar headgroup.
- major component of cellular membranes and vesicles; lyso-PLs have only one FA
- Headgroups vary by charge, cellular location, and effects on membrane curvature and protein function.
- PLs are also precursors of lipid second messengers: position specific cleavage of PIP 2 by phospholipases generates bioactive molecules such as diacylglycerol and
inositol-1,4,5-P
Define sphingomyelin and glycosphingolipids?
Sphingomyelin and glycosphingolipids (e.g. cerebrosides, gangliosides) contain a sphingosine backbone; they have signaling or recognition roles and are abundant in the
brain
Genetic disorders of glycosphingolipid
degradation
Glycosphingolipids (GSLs) are synthesized and degraded in strictly ordered pathways: genetic defects in lysosomal
GSL degradation causes severe neurodegenerative diseases
What do you know about cholesterol?
- Cholesterol is important for maintaining lipid bilayer fluidity. Derived from diet or made endogenously from isoprene
- Cholesterol is highly insoluble and must be transported in lipoproteins, imbalances in which cause atherosclerosis and vascular diseases
- The liver coordinates intercellular transport and regulation of cholesterol; in humans, cholesterol is excreted, not degraded
Lipoproteins allow for __________ and __________ transport. Explain.
- allow for triacylglycerol and cholesterol transport
- TAG’s and cholesterol are packaged as lipoproteins when in circulation to allow for transport
- TAG in lipoproteins are used as a fuel source or stored in adipose tissue
Cholesterol derivatives?
Cholesterol is a precursor of bile acids, steroid
hormones and vitamin D Isoprenoids (derived from cholesterol intermediates) include dolichol and ubiquinone
Why do lipids spontaneously associate in water? What structures can be formed?
- lipids spontaneously associate in water due to their amphiphilic or hydrophobic nature, but adopt many different structures depending on their size, shape, charge
These structures include:
- droplets (TAGs)
- micelles (FFAs, lyso-PLs)
- vesicles (PLs)
- bilayers (PLs)
- monolayers (air-water interface)
Note:
Micelle-forming lipids can act as detergents: solubilizing membranes, grease, etc., to release components