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tru_cell > module 2 > Flashcards

module 2 Flashcards

1
Q

Why is it that you can overcome enzyme inhibition of a competitive inhibitor by adding an excess of substrate, although this will not have any effect on a non-competitive inhibitor

A

In competitive inhibition, the structurally similar molecule to the substrate competes with the substrate for binding at the active site of the enzyme. If you add more substrate to the solution, there will be more substrate than the competing molecule and therefore substrate will be more likely to bind at the active site.

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2
Q

The KM for the reaction of chymotrypsin with N-acetylvaline ethyl ester is 8.8 x 10-2 M, and the KM for the reaction of chymotrypsin with N-acetyltyrosine ethyl ester is 6.4 x 10-4 M. For which substrate does the enzyme have the higher affinity

A
  • The lower Km the higher the affinity, because KM is the substrate concentration at which the reaction is running ath ½ Vmax. Therefore, lower KM means that we need less substrate to get to ½ of Vmax.
  • Therefore, the enzyme has a higher affinity to N-acetyltyrosine ethyl ester
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3
Q

Feedback inhibition typically alters the activity of the first enzyme of a metabolic pathway, rather than one of the later enzymes of the pathway. Why is this adaptive?

A

By inhibiting the initial step of the reaction, we make sure that we do not waste energy producing intermediates that are not going to be used.

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4
Q

In the reaction A + B <—> C + D:

How might the reaction occur in the cell if the DG is very positive?

A

G is via coupling. This reaction might occur in the cell if it is coupled with the reaction that is very exergonic (has very negative DG) and leads to the overall negative DG

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5
Q

What would ATP synthase do if H+ ions were raised to a high concentration in the mitochondrial matrix and simultaneously decreased to a low concentration in the intermembrane space

A
  • Concentration of H+ ions is higher in the intermembrane space and would normally be pumped into the matrix since the concentration is lower there through the ATP synthase that would
  • in the given situation, ATP synthase would pump H+ ions from matrix into the intermembrane space to reach the equilibrium. Simultaneously, ATP would be hydrolyzed and ADP would be produced
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6
Q

Determine which of the substances PQH2, P680+, and A-0 is:

a. The strongest oxidizing agent
b. The strongest reducing agent
c. A mobile electron carrier

A
  1. P680+
  2. is A-0
  3. PQH2 is the mobile electron carrier that carries electrons between PSII and cyt b6
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7
Q

An investigator radioactively labels CO2 with 14C. He exposes a plant from a temperate climate to the radiolabeled CO2.

In what molecule does the 14C first appear to accumulate stably

A
  • looking at C3 plants
  • radiolabelled C from CO2 will be combined with initial receptor (RuBP) and the newly formed molecule will be rapidly converted into PGA (3 C molecule; also an intermediate in glycolysis).
  • C+RuBP->PGA
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8
Q

An investigator radioactively labels CO2 with 14C. He exposes a plant from a temperate climate to the radiolabeled CO2.

  1. Where does the 14C appear in a plant that is well adapted for life in a hot, dry habitat?
A
  • c4 plants
  • intermediate produced is a 4-carbon molecule (oxaloacetate or malate
  • This intermediate allows C4 plants to open and close their stomata in response to the climate
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9
Q

What do plants do to prevent water loss in a hot, dry climate

A
  1. C4 plants
  • producing four-carbon intermediate that allows them to open and close their stomata
  • closed stromata-> no gas exchange-> no h2o loss/no CO2 diffusion
  • can fix CO2 even when its concentration is very low (via PEP carboxylase in mesophyll cells
  1. CAM plants
    * stomata is closed during the day (to avoid water evaporation) and is open at night
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10
Q

photorespiration in C3 plants in hot climate

A
  • RuBP has higher affinity to O2 in hot and dry climate allowing O2 fixation
  • O2 concentration would be increasing in the hot
  • rubisco uses O2 as a substrate leading to photorespiration in C3 plants
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11
Q

why are C4 plants immune to
photorespiration

A

C4 plants are protected from photorespiration due to the following adaptations:

  • Use different enzyme for CO2 fixation (PEP carboxylase) found in mesophyll cells
  • PEP carboxylase has no affinity for O2 and can work on lower CO2 concentration level
  • PEP carboxylase enables C3 plants to fix CO2 at the lower levels of CO2 present when the stomata are closed during the heat day
  • Fixed CO2 is then transferred to bundle sheath cells ->splits from carrier producing high level of CO2 ->Rubisco produces carbs in Calvin cycle
  • Having spatial arrangements enables PEP pathway to fix CO2 at much lower CO2 concentration and then send this fixed CO2 to another area that contains Rubisco (bundle sheath cells) that function at higher CO2 levels
  • In bundle-sheath cells Rubisco is not exposed to O2
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12
Q

types of rxn dep on Gibbs

A
  • ΔG<0: exergonic rxn; spontaneous; proceeds towards the lower state of E
  • ΔG>0:endergonic rxn; nonspontaneous ; thermodynamically unfavourable
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13
Q

how t would impact rxn rates

A
  • At lower t rxn rates rise w/ increasing t due to higher E of the reactants
  • At higher t, rxn rates decrease due to denaturation of the enzymes
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14
Q

enzyme inhibition

A
  1. competitive: V max const, increase in Km
  2. noncompetitive: lower V max, same Km
  3. uncompetitive: decrease V max and Km
  4. mixed: decrease in V max, increase/decrease in Km
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15
Q

Enzymes can be very specific in the reactants they can bind and the reaction they catalyze. How are they capable of doing this? Why is this specificity important?

A
  • Enzymes are capable of binding one or a small number of closely related biological molecules b/c the strucute of the active site is very specific
  • Specificity is most important in terms of making sure that enzymes only work on one molecule of a very small group of molecules. It is crucial to maintain order within the cell at the particular time
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16
Q

catabolic vs anabolic pathways

A

catabolic:

  • Convergent b/c even though the substrates begin as macromolecules having very different strucutre, they are converted by catabolic pathways to the same low-molecular-weight metabolites
  • anabolic: divergent b/c the pathway starts from a few precursors and utilize ATP to synthesize large variety of cellular materials.
17
Q

Feedback inhibition

A

type of allosteric inhibition in which enzyme catalyzing the first comitted step in a metabolic pathway is temporarily inactivated when the concentration of the end product of that pathway reaches a certain level; it is important b/c it keeps the cell from wasting E and materials by producing compounds that are not utilized; exerts an immediate sensitive control over a cell’s anabolic activity

18
Q

Compare b/ properties of outer and inner mitochondrial membranes:

A

Outer: encloses mitochondrion, serves as outer boundary, hihgly permeable due to the presence of porins

Inner: hihgly impermeable; highly invaginated (to increase the surface area to house ETC needed for aerobic respiration)

19
Q

Compare b/ properties of intermembrane space and the matrix:

A
  • Matrix: gel-like consistency due to the high concentration of water-soluble proteins; contains ribosomes, RNA, DNA
  • Intermembrane space: expands under conditions of active respiration; contains several enzymes; contains H+ from the ETC that are used to produce ATP via ATP synthase
20
Q

How do pyruvate contribute to aerobic respiration in the mitochondria:

A
  • Transported from the cytoplasm where it is formed, diffuses thry the outer mitochondrial membrane and actively transported thru the inner mitochondrial membrane
  • In the mitochondrial matrix it is decarboxylated to form Acetyl-CoA which is used in the Kreb’s cycle
21
Q

how NADH contribute to aerobic respiration in the mitochondria:

A

NADH:

  • High E e carried by the NADH formed gy glycolysis are used by malate-aspartate shuttle to reduce mitochondrial NAD+ to form NADH or are transformed into mitochondrial FADH2 from FAD (also by malate-aspartate shuttle
  • Mitochondrial formed NADH and FADH2 are used in the ETC
22
Q

Why is TCA considered to be central pathway in E metabolism of the cell?

A

b/c all of cell’s energy-providing macromolecules are broken down into metabolites of the TCA cycle

23
Q

Chemiosmosis:

A
  • the coupling of H+ translocation to the ATP synthesis
  • Mechanism of ATP synthesis whereby the movement of elecctrons through an ETC result in the est of proton gradient across the inner mitochondrial membrane, with the gradient acting as ahigh E intermediate linking oxidation of substrates to the phosphorylation of ADP.
24
Q

Peroxisome:

A

Simple membrane-bound organelles

Contain dense, crystalline core of oxidative enzymes

Plant seedlings contain a specialized form of peroxisome called glyoxysome (provides energy and material to form new plant

Functions:

Oxidation of long fatty acids

Synthesis of plasmalogens (an important class of phospholipids in the brain tissue), luciferase

Synthesis and degradation of hydrogen peroxide

25
Q

Oxidative phosphorylation vs Substrate-level phosphorylation:

A

Oxidative phosphorylation:ATP formation is driven by E that is released from electrons

removed during substrate oxidation

Substrate level phosphorylation:

ATP is directle formed by transfer of a phosphate group from a substrate molecule to ADP

26
Q

What are the major activities during aerobic respiration in the mitochondria?

A
  • Incorporation of the product of glycolysis into the TCA cycle (via PDC)
  • Krebs cycle
  • ETC that generates a proton gradient
  • Synthesis of ATP by the ATP synthase
27
Q

Overview of photosynthetic metabolism:

A
  • Light dependent rxns: E from sunlight is absorbed and stored as chemical E in ATP (primary source of chem E) and NADPH (primary source of reducing power)
  • Light independent step: synthesis of carbs from CO2 using E stored in APT and NADPH
    *
28
Q

Difference b/ structure of chloroplast and mitochondria:

A

Chloro carry out theiir E conversions by means of proton gradients in the same way as mitoch

Chloro bigger than mito

Both have permeable outer membrane and impermeable inner membrane. Mito inner membrane is folded, while chloro is not

Inner membrane of mito houses the machinery for oxidative phosphorylation, but in chloro the machinery for photosynthesis is in the thylakoid membrane

Stroma of the chloro is analogous to the matrix of the mito (both contain enzymes, ribosomes, RNA and DNA)

Majority of the proteins in the chloroplast and mito are encoded by nuclear SNA and are synthesized in the cytosol

29
Q

Photosystems:

A
  • Spatially separated pigments complex
  • The light-absorbing pigments are held together with large multiprotein complexes
  • Where the light absorbing rxns occur
  • Photosystems act in series
  • When sunlight strikes thylakoid, E is absorbed by antenna pigment of both systems and passed to the rxn centers of both systems -> e transferred to the primary e acceptor-> separation of charges occur (rxn center gets +)
  • Separation of charges is the light reaction
  • Both photosystems boost E from a lower level to higher
  • Two types are required to catalyze the light-absorbing reactions:

Photosystem II (PSII):

  • Booosts electrons from energy level below that of water to a midway point
  • Reaction center: P680 (pigment that absorbs 680 nm)

Photosystem I (PSI):

  • Raises electrons from the midway point to an energy level well above that of NADP+
  • P700
30
Q

Photosystem II (PSII)

A
  • Booosts electrons from energy level below that of water to a midway point
  • Reaction center: P680 (pigment that absorbs 680 nm)
  • Protein complex that absorbs light energy ( involving P680, chlorophyll and accessory pigments
  • Transfer electron water->plastoquinone
  • Works in dissociation of water and produces proton and O2
  • Cyclic photophosphorylation
  • photolysis
  • Hydrolysis of water and ATP synthesis
  • Raises electrons from midway point to an energy level well above that of NADP+
  • core composition: Two subunits made up of D1 and D2
31
Q

Photosystem I (PSI)

A
  • Raises electrons from the midway point to an energy level well above that of NADP+
  • P700
  • Uses light E to convert NADP+ to NADPH2

Involves P700, chlorophyll and other pigments

  • Outer surface of thylakoid membrane
  • Cyclic and non-cyclic photophosphorylation
  • function:

NADPH synthesis

Boosts electrons from energy level below that of water to a midway point

  • core composition: psaA, psaB
32
Q

What is the advantage of having different pigments to absorb light?

A
  • It allows light absorption and electron excitation at various wavelengths
  • Ensures that a greater percentage of incoming photons from the different wavelength of light will stimulate photosynthesis
33
Q

How does the proton gradient generated in the light-dependent rxn of photosynthesis lead to the formation of ATP?

A
  • The mechanism of ATP synthesis in the chloroplast is identical to that in mitochondria
  • Protons move from higher concentration in lumen thru the ATP synthase into the stroma which drives the phosphorylation of ADP
34
Q

main part of Calvin cycle

A
  1. Carboxylation of RuBP to form PGA
  2. Reduction of PGA to the level of sugar (CH2O) by the formation of GAP using NADPH and ATP produced in the light-dependent rxn
  3. Regeneration of RuBP which also requires ATP
35
Q

Photorespiration:

A
  • O2 attached to Rubisco->2-phosphoglycolate->glycolate->transferred to peroxisome->release of CO2
  • Leads to release of previously fixated CO2
  • Series of rxns in which O2 is attached to RuBP and eventually results in the release of fixed CO2 from the plants
  • Waste of plants E and is common in C3 plants
36
Q

What are the adaptations of C4 to reduce photorespiration?

A
  • Use different enzyme for CO2 fixation (PEP carboxylase) found in mesophyll cells
  • PEP carboxylase has no affinity for O2 and can work on lower CO2 concentration level
  • PEP carboxylase enables C3 plants to fix CO2 at the lower levels of CO2 present when the stomata are closed during the heat day
  • Fixed CO2 is then transferred to bundle sheath cells ->splits from carrier producing high level of CO2->Rubisco produces carbs in Calvin cycle
  • Having spatial arrangements enables PEP pathway to fix CO2 at much lower CO2 concentration and then send this fixed CO2 to another area that contains Rubisco (bundle sheath cells) that function at higher CO2 levels
  • In bundle-sheath cells Rubisco is not exposed to O2
37
Q

Rubisco:

A
  • Function: fixation of CO2 into 6C compound RuBP
  • It is highly concentrated in chloroplast b/c the rate of turnover for this enzyme is very slow and therefore high concentration is needed
38
Q

PQH2

A

mobile carrier that carries electrons between PSII and cyt b6

39
Q

Photorespiration

A
  • Take up oxygen
  • Releases some carbon dioxidd
  • Rubisco oxygenates RuBP

tru_cell (6 decks)

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