Self Help Questions

1) How many stages of cellular respiration are there?1. glycolysis2. krebs3. electron transport

2) What is acetyl CoA and why is it so important in the metabolism of ‘energy’?

Sugars, amino acids, fatty acids pass through this molecule on their way to becoming water and carbon dioxide. This intermediate is used in the synthesis of the major biomolecules. Center in molecule in metabolism

3) In which steps of the Krebs cycle are electrons abstracted?Pyruvate---Acetyl CoA = NADHIsocitrate---a ketoglutarate = NADHA keto glutarate---succinyl CoA = NADHSuccinate---fumarate = FADH2Malate---Oxaloacetate = NADH

4) What is the ultimate fate of these electrons?The electrons are passed from coenzyme Q to a series of proteins called cytochromes and eventually to oxygen.

5) What does the electron flow do?Creates a proton gradient. (complex I, III, IV) The energy will be turned into a proton gradient that is used to make ATP.

6) What is oxidative phosphorylation?Process for generating ATP, it depends on the creation of a pH gradient within the mitochondrion as a result of electron transport

7) How many molecules of ATP are associated with glucose oxidation? 30 for Glycerol Phosphate shuttle

32 for malate aspartate shuttle 8) Is oxygen involved in the Krebs cycle?

NO!!!!!9) What is biological oxidation? Is oxygen always involved?

10) What is a mitochondria? How many membranes does it have? Are they both permeable?

An organelle that contains the apparatus responsible for aerobic oxidation of nutrients; site of oxidative phosphorylation in cell; ADP is phosphorylated to give ATP- electron transport and ATP synthesis are strongly coupled; 2 membranes;

inner membrane is highly impermeable (this allows for oxidative phosphorylation)

11) What is the matrix?Inside if mitochondria (low H+ concentration; high pH); all of krebs cycle takes place here except for one step

12) Which step of the Krebs cycle occurs in the inner membrane?Succinate----fumarate FADH2 is generatedRest of cycle occurs in matrix

13) List the different kinds of redox centers found in the respiratory chain.Complex I: NADH-CoQ oxidoreductaseComplex II: Succinate-CoQ oxidoreductaseComplex III: CoQH2-cytochrome c oxidoreductaseComplex IV: Cytochrome oxidase (?)

14) Where is cytochrome-C situated? How is it located here? Why is it here?Cyt c is not part of any complex. It is loosely bound, a water soluble electron carrier on the outside of the inner mitochondrial membrane. Heme group allows for transfer of only 1 electron at a time.

15) Why is NADH described as a two electron carrier?Nicotinamide adenine dinucleotide (NAD+) : H+ and 2e- or write H- (a hydride) this is two electrons and a proton. 2 Hydrogens at top of molecule.

16) FAD is described as a prosthetic group? What does this mean? FAD is a prosthetic group, that is permanently part of the pyruvate dehydrogenase complex

17) Show how FAD or FMN can transfer one or two electrons. (you don’t have toknow this but its good to try)** see notes***

18) Why is ubiquinone lipid soluble?The molecule is lipophilic with a conjugated ring and aliphatic chain(aka isprenoid units). Needs to move freely within membrane to accept electrons from Complex I and II.

19) Show why ubiquinone can transfer one or two electons.See page 10 (slide 30) of Electron Transport handout. This is very similar to FADH2. Has two carbonyl groups para to each other on the ring. Once two electrons are bound (2H) then the ring is aromatic.

20) How many cytochromes are there? Cytochrome Bh, BL ( Complex III)Cytochrome C1 (moves between III IV)Cytochrome A, A3 ( Complex IV) 5 total

21) What is a heme group? What metal does it contain?It contains iron and this is either oxidized Fe III or reduced Fe II Heme is a prosthetic group of cytochromes. Heme contains an iron atom embedded in a porphyrin ring system

22) How is iron bound to non heme iron proteins?

The iron is usually bound to cysteine or to sulfer clusters(example in complex I)

23) What electron carriers are non-heme iron proteins associated with?

24) What do copper ions do in the respiratory chain? Where are they found?Copper ions are intermediate electron acceptors that lie between the two a-type cytochromes in COMPLEX IV

25) How is energy stored in molecules? High energy bondsAsk HIM!

26) What forms of ‘energy’ do we see in the respiratory process?Electrical, chemical, potential?

27) Name five different types of electron carrier found in the respiratory chain.

NADH, FADH2, CoQ, Cyt C, Fe-S

28) Can all cytosolic molecules enter the matrix?No

29) Does NADH produced in the cytoplasm during glycolysis enter the matrix? If nothow does this NADH get to the respiratory chain?

NADH cannot enter the matrix2 shuttle mechanisms to transport NADH into inner membrane (glycerol phosphate shuttle(GAP)-- forms FADH2 inside inner membrane = 1.5 ATP) & (malate-aspartate shuttle-- forms NADH inside inner membrane = 2.5 ATP). FADH2(from GAP) and NADH(from malate) then go to electron transport chain.

30) Does ATP freely diffuse out of the matrix into the cytoplasm?

31) Where is pyruvate formed? cytoplasm

32) Where is pyruvate degraded to CoA?Inner membrand space?

33) Where is NADH and FADH2 from CoA?Matrix?

34) Where is the electron transport chain?Inner mitochondrial membrane

35) Why is the transport chain so complicated?More control points, more steps = more energy for ATP productionNot sure if correct?

36) How do the redox potentials of the various electron carriers vary?Complex I = -81 kJ mol-1 ** strongly exergonic and sufficient to drive the phosphorylation of ADPComplex II = -13.5 kJ mol-1 no protons are pumpedComplex III = -34.2 kJ mol-1 **strongly exergonic & sufficient to drive the phosphorylation of ADPComplex IV = -110 kJ mol-1 ** catalyzes final step of e- transport (from cyt C to oxygen)

37) Why are there many steps of electron transport?

38) How many complexes are the in the transport chain? 4 complexes

39) Which Krebs cycle enzyme is in the electron transport chain?Succinate dehydrogenase

40) Where does ubiquinone collect electrons?Complex I & II

41) Where does ubiquinone deliver electrons?Cyt c (complex III)

42) What does cytochrome C do?Carries electrons from III to IV

43) Which complexes generate the proton gradient?I, III, & IV

44) Does complex II reduce NADH?No, FADH2 . Complex I oxidizes NADH to NAD; NAD was reduced to NADH in glycolysis and in the TCA .

45) How does a proton gradient drive the synthesis of ATP?

The proton pumping created a pH gradient and an electrochemical potential (voltage drop) across the inner mitochondria membrane. The chemiosmotic coupling mechanism is based entirely on the difference in proton concentration between the inner mem space and matrix. Protons go through the F0 channel of the ATPase and drive the F1 wheel to produce ATP.

46) Which step in glycolysis yields ATP? 1,3 BPG3-phosphoglyceratePEPpyruvate

49) How is food breakdown in cells coupled to supply energy-requiring reactions inthe cell?

Molecules containing a high energy phosphate compound store the energy from food oxidation. The energy in these bonds is harnessed to drive all the energy requiring process in the body.

50) What is a high-energy phosphate compound?a delta G that is greater than 30 kJ/mol

51) What are the structural features of high-energy phosphate compounds?Usually a lot of energy caused by repulsion from the many phosphate (-) charges. The molecule finds resonance stability on its own and via salvation.

52) What transports the high-energy phosphate around the cell? AMP or ADP

53) How does ATP perform chemical work? The hydrolysis of ATP to ADP releases energy (-30.5 kJmol-1)Kinetically stable in cell; not used until needed (enzymes get involved) **hydrolysis on its own would take a week!!)

54) How does ATP drive other types of work?It is coupled to other reactions.

64) How is the free energy released by electron transport used to form ATP?

The energy-releasing oxidations give rise to proton pumping, which creates a pH gradient. The proteins of the respiratory complexes take up protons from the matrix to transfer them to the redox reactions, which then transfer protons through to the inner membrane space.

65) How are protons ejected?

Protons are ejected in only one direction (into inner membrane space) by electron carriers.

66) How is ATP generated from proton flow?ATP synthase couples the proton gradient to ATP synthesis. (this protein is not part of the ETC) ATP production depends on ion channels through the inner membrane. Protons flow back into the matrix through the Fo channel of ATP synthase (energy in gradient drives protons back) and the F1 unit forms ATP.

**conformational coupling mech: proton flux drives the release of tightly bound ATP

55) Why are cell membranes needed?

To hold together the contents of the cell and to compartmentalize cells.Functions of membranes:

Transport of substances in and out of the cellSignal transductionMaintaining the shape of the cellCell-cell interactions

56) What are the polar lipid constituents of cell membranes?

Glycerophospholipids: membrane lipid containing glycerol; attached one finds the highly polar head group, phosphonyl. Phosphonyl can have other polar groups attached to it (groups are listed in the following questions).

57) What are the polar groups attached to the phosphatidic acid?**see Handout 8 page 4 for the pictures of polar groups**Phosphatidyl ethanoloaminephosphatidyle choine (PC)phosphatidyle serine (PS) inositolcardiolipin

58) Why are there so many different types of membrane lipids?

They allow for different membrane properties. (PC has a positive charge, PS has a negative charge, cerebrosides have no charge.) The two bilayers may have different lipid compositions, e.g., glycolipids (sugars always on the outside of the cell in the external aqueous environment)

59) What are fatty acid component of membrane lipds?

Phosphatidic acid: two fatty acids esterified to glycerol-3-phosphate make up the nonpolar hydrophobic tails. These tail components are not fixed; they range from C14 to C24 (C14-C18 are most common).**usually the fat attached to the C1 C is saturated; to the C2 C is unsaturated (cis-which introduces a kink).

60) What is cholesterol doing in membranes?

Cholesterol is elongated with a rigid steroid nucleus and flexible hydrocarbon chain. It is an amphipathic molecule, the –OH group being weakly polar. It acts as a “fluidity buffer,” i.e. it prevents close packing of the hydrocarbon chains and thereby lowers the melting point of the membrane.

61) The self sealing character of the lipid bilayer

A two-dimensional fluid; it gives cells flexibility and self sealing potential (cell division). Also involved in endo- and exocytosis.

62) Permeability characteristics of the lipid bilayer

The ability of a molecule to diffuse through a lipid bilayer is related to its fat solubility.

Strongly polar molecules such as ions traverse slowly; large more weakly polar molecules (glucose) require a transporter but are still slow; ethanol, glycerol= fast.

Water molecules must be stripped off of polar/ionized groups (this is unfavorable) Almost impermeable to ions (slow leakage does occur) Water molecules (despite being polar) pass through the lipid, sufficiently easy for

the needs of the cell. Some cells contain aquaponin (renal cells) Gases such as oxygen readily diffuse.

67) Peroxisomal oxidation of fatty acids

68) What are neutral fats (a triacyl glycerol)?

The storage form of fatty acids (not found in membranes because they have no polar head groups and therefore can only form oil droplets). Three molecules of fat are esterified to the three hydroxyl groups of flycerol. TAGS are suitable as food.

69) What are lipids?

Heterogeneous class of naturally occurring organic compounds classified together on the basis of common solubility properties; insoluble in water; soluble in aprotic organic solvents (diethyl ether, chloroform, methylene chloride, acetone)

71) What are ceramide, sphingomyelin , cerebrosides, GangliosidesThese are based on glycerol. Evolution has provided another molecule with overall similar shape which is derived from sphingosine.

Ceramide: C-2 hydroxyl group of glycerol is replaced an NH2 (another tail is added after) ; C-1 is replaced by a C15 hydrocarbon;

Sphingomyelin: take Ceramide and add a phosphoryl choline (PC) to C-3 of glycerol

Cerebrosides: take sphingomyelin and on the phosphate head put galactose or glucose (this is now highly polar)

Gangliosides: different sugars are likened together in a branched oligosaccharide structure (have highly polar head groups). Involved in determining human blood groups O, A, B.

**see Handout 8 page 5-7 for pictures**

73) What movements can lipids make?

Lipids can move in 2 dimensions (think of movement through a crowd of people); transverse movement- lipids have the potential for rapid lateral movement within the plane of the bilayer.

77) How are Membrane Proteins Designed?

Proteins can be inserted into membranes provided they have the requisite properties.

78) What is the Lipid fluid mosaic model?

This describes the interaction of lipids and proteins in biological membranes; proteins “float” in the lipid bilayer. Fluid: lateral motion of components in membrane. Mosaic: components exist side-by-side as separate entities.

79) What holds integral proteins in the lipid bilayer?

Bound tightly to the interior of the membrane; removed by treatment with detergents or ultra sonification (this generally denatures them)

80) How are peripheral membrane proteins anchored to membranes.

Bound by electrostatic interactions; can be removed by raising the ionic strength.

81) What are Glycoproteins?

Proteins with a sugar (branched oligosaccharides) attached at the exterior surface.

82) Define the functions of membranes.

Allow specific substances to be transported in and out of the cell; provide the right environment for a number of proteins to function properly (proteins regulate dynamic functions). Surface protects cell from potential hostility.

83) How are substances transported in and out of the cell.Channels, transporters, pumps, receptors

84) What is passive transport or facilitated diffusion?

Passive: movement through membrane driven by a concentration gradient (the molecule or ion moves directly through a channel protein in the lipid bilayer by simple diffusion). Small, nonpolar molecules traverse fast; does not require energy

Glucose transporter- allows glucose to diffuse passively across the membrane.

Gated pores or channels Na+, K+, Ca2+ - tansport signals for specific ions that open/close on receipt of a signal (voltage or ligand gated)

85) What is Active Transport

Transport that requires performance of work which involves ATP hydrolysis.

Describe the Mechanism of the Na+/K+ pump.

87) How does knowledge of the thermodynamics of a chemical reaction help usdetermine whether it will occur or not?

The overall delta G for coupled reactions is the arithmetic sum of the delta G values of the component reactions. A favorable negative change in free energy (value is negative) is required for the rxn to occur.

88) How does a molecule store energy?

As a result of catabolic reactions of food molecules, inorganic phosphate ions are converted into phosphoryl groups in molecules of a high-energy phosphate compound. This molecule is transported wherever work is to be performed in the cells where the phosphoryl groups are converted back to inorganic phosphate ions with the liberation of the free energy that went into formation of the phosphate compound.

89) How do the concentration of reactants or products influence the direction of areaction?

Yes. As concentration of products increases, the formation of products will decrease until product is removed.

Delta G = delta G’ + RT ln (prod/react) ATP levels are ~2-8mM, ADP levels ~0.2-0.8 mM, Pi levels ~2-8mM

90) Do enzymes change the overall thermodynamics of a reaction. If so how? Whatabout the kinetics of a reaction? If so how?

Yes, they lower the activation energy

91) How is the energy from food combustion stored?Energy from food oxidation is stored as a high-energy phosphate compound. The energy in these bonds is harnessed to drive all the energy requiring processes in the body.

92) Define low and high energy molecules.

Low energy: delta G 4-20 kJ mol-1High energy: delta G > 30 kJ mol -1

93) What is the free energy of hydrolysis of a typical phosphate ester?

~12.5 kJ mol-1

94) Draw a phosphate anhydride. What is the ∆G for the hydrolysis?

~33.5 kJ mol-1

**know the structure of the steroid