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biochem 200 > Final > Flashcards

Final Flashcards

1
Q

what is the reaction for nitrogen fixation? What are the two places you find nitrogen fixation and what are the conditions for each?

A

N2 + 3H2 -> NH3. can be an industrial process (200 atmospheres and 400 degrees) or a bacterial process (atmospheric pressure, ambient temp)

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2
Q

what are two ways a reaction can be accelerated? what is a potential problem?

A

adding heat or adding a catalyst. problem with this is that when you add heat, you increase all reactions and not just the ones you want

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3
Q

what kind of proteins are enzymes, and what kind of strucutres do they have?

A

typically globular proteins, can have 1,2,3,4 structure

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4
Q

what are some properties of enzymes?

A

they accelerate reaction rates, are regenerated at the end of the reaction, 10^6 to 10^20 fold increases in reaction rates, they are highly specific (no side reactions)

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5
Q

are enzymes regulated? what does this mean?

A

enzymes are regulated. this distinguishes them from other non biological catalysts. they have flexible structures. changing the shape of an enzyme changes its function

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6
Q

regarding free energy, when will a reaction proceed forward?

A

will only proceed if the free energy of the products is less than the free energy of the reactants (delta G is negative). this is an exergonic reaction and thermodynamically favorable

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7
Q

what is the activation energy / activation barrier

A

the energy required to reach the transition state from the ground state of the reactants

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8
Q

what is the transition state?

A

most critical for determining how fast a reaction will go, it has the highest free energy because it is most unstable. occurs at the peak of the activation barrier (the energy level that must be exceeded for the reaction to proceed). a lower barrier means the more stable the TS and the more often the reaction proceeds

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9
Q

what do enzymes effect and what do they not effect?

A

enzymes reduce the free energy of the transition state, but DO NOT EFFECT THE FREE ENERGY CHANGE OF THE REACTION

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10
Q

what are the four ways in which enzymes reduce the free energy of the transition state?

A
  1. removing substrate from aqueous solution (desolvation) 2. proximity and orientation effects 3. taking part in the reaction mechanism 4. stabilizing the transition state
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11
Q

what is the active site and what is located in it and what is it important for? what is it complementary to?

A

region of enzyme where catalysis occurs. usually only a small portion of the protein. where the key amino acids are located (binding and catalysis). important for affinity, specificity and rate. complementary to substrate/TS

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12
Q

what does the design of the active site contribute to? what happens in the absence of a substrate?

A

affinity and specificity. active site changes in the absence of a substrate

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13
Q

what is desolvation and what are 3 advantages?

A

exclusion of water. advantages are that it accelerations the reaction, enhances polar interactions (h bonds and ion pairs), and prevents side reactions.

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14
Q

what does the exclusion of water do in the induced fit model?

A

in induced fit (where the enzyme changes shape when substrate binds), even more water is excluded and catalytic groups can come together

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15
Q

how do enzymes effect proximity and orientation?

A

chemical reactions only occur if substrates come together in the right orientation. the active site of enzymes bring substrates close to each other and in the correct geometry

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16
Q

what are the ways ionizable side chains participate in chemical catalysis? how is this achieved?

A

some enzymes participate in reactions by positioning functional groups near the substrates in the active site. these groups can function as: acid base catalysts, covalent catalysis, metal ion catalysis. achieved through amino acids or cofactors (or both)

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17
Q

what do amino acid side chains do in acid-base catalysis? what about covalent catalysis?

A

these groups can act as acid or base catalysts, depending on their state of protonation. in nucleophilic catalysis, they can act as nucleophiles when they are in their deprotinated states

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18
Q

what is a coenzyme? what are two types of coenzymes and how do they differ?

A

coenzymes are organic cofactors. the two types of coenzymes are cosubstrates and prosthetic groups. cosubstrates are converted and released (not a permanent part of the structure). prosthetic groups are converted in the active site and then restored

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19
Q

do enzymes bind substrates better or the transition state? why? what is this called?

A

bind the transition state better, because the TS is more unstable and will release more energy. called preferential transition state stabilization

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20
Q

what is a reasons transition state analogs are potent inhibitors of many enzymes? when is this used?

A

bind to enzymes with higher affinity compared to substrate. rational basis for drug design

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21
Q

what does km (michaelis constant) mean? what does a low value mean? how is km represented on a graph?

A

km is a measure of the affinity of the enzyme for the substrate. the lower the value of Km means the more tightly the substrate is bound. km is also a parameter that determines the shape of V0 vs [S], it is the substrate concentration when the initial velocity is one half the Vmax value

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22
Q

what is competitive inhibitions for enzyme activity?

A

substances that bind reversibly in the active site. they resemble the substrate or transition state (substrate analogue or TS analogue) but do not react.

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23
Q

how do competitive inhibitors block enzyme activity? what does this cause?

A

they physically block the active site. causes an apparent decrease in the affinity for enzyme and substrate (increase km)

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24
Q

how do you overcome competitive inhibition?

A

increasing substrate concentration will overcome inhibition (note that vmax does not change)

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25
Q

why dont inhibitors in competitive inhibition actually react?

A

they are similar to the substrate in shape and size but differ chemically

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26
Q

what are allosteric enzymes? what kind of structure do they usually have?

A

enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site. usually are oligomeric (quaternary structure)

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27
Q

what kind of relationship do allosteric enzymes show between reaction velocity and substrate concentration

A

sigmodial relationship

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28
Q

heteroallostery

A

an allosteric enzyme’s catalytic activity is modulated by the noncovalent binding of specific molecules at a site other than the active site

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29
Q

what are the two states of an allosteric enzyme?

A

T (tense, low activity) and R (relaxed, high activity)

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30
Q

which way would the sigmodial curve move if the allosteric enzyme was inhibited or activated?

A

inhibited would shift to the right, activated would shift to the left

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31
Q

covalent modification of an amino acid residue changes the ___ structure of enzymes? what is the most common type of reversible covalent modification?

A

tertiary. phosphorylation is the most common

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32
Q

what happens in phosphorylation?

A

Ser/Thr/Tyr OH becomes phosphorylated. this increases the size, polarity and charge significantly

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33
Q

what enzyme catalyzes the phosphorylation of proteins? what catalyzes the dephosphorylation?

A

protein kinase for phosphorylation, protein phosphatases dephosphorylates

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34
Q

what are lipids?

A

non polar, hydrophobic, insoluble in water compounds

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35
Q

what compounds are considered lipids?

A

fatty acids, triaclyglycerol, membrane lipids, cholesterol

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36
Q

what are fatty acids? what word can they be described as? are they saturated or unsaturated?

A

long chain hydrocarbon carboxylic acids (up to 24 long). general formula CH3(CH2)nCOO-. “amphipathic”. may be saturated or unsaturated (cis)

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37
Q

what are the three named carbons on a fatty acid and where are they located?

A

the alpha carbon is the one attached to the carboxylate, beta is the next carbon in the chain, omega is the last carbon in the chain

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38
Q

what happens to the melting point as the number of carbons increases in fatty acids?

A

melting point increases

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39
Q

what happens as you start introducing double bonds in the fatty acid? is this process more or less dramatic than length?

A

introduction of double bonds makes the melting point lower. more dramatic than length, has a greater effect on melting point

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40
Q

why do unsaturated fatty acids have a lower melting point?

A

they cannot pack together as effectively because of the bend in the unsaturated chain

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41
Q

what are fatty acids stored as?

A

triacylglycerol (TAG) is a way of storing fatty acids. tag is very hydrophobic (not amphipathic)

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42
Q

what is triacylglycerol formed from?

A

three acyl chains attached to glycerol

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43
Q

what are three types of membrane lipids?

A

glycerophospholipids, sphingolipids, cholesterol

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44
Q

are glycerophospholipids amphipathic? why?

A

presence of large polar group makes them amphipathic

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45
Q

what % of membranes does cholesterol account for?

A

35%

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46
Q

what is the structure of cholesterol like? is it amphipathic?

A

rigid, non polar structure (hydrocarbon/ring structure). it is weakly amphipathic, has one OH group (mostly hydrophobic with 27 carbons and one OH)

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47
Q

what does cholesterol do in membranes?

A

maintains fluidity and rigidity. OH associates with polar head groups of other lipids, and the non polar portions are found in the membrane.

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48
Q

what do amphipathic molecules form in water? what do membrane lipids do vs fatty acids? what are these arrangements useful for?

A

amphipathic molecules form micelles or bilayers in water. fatty acids form micelles and membrane lipids form bilayer. arrangements eliminate unfavourable contact between water and hydrophobic tails, yet permit solvation of polar head groups

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49
Q

what do lipid bilayers form?

A

spherical vesicles called liposomes

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50
Q

what is the transition temperature for a lipid bilayer? what does it depend on?

A

the temperature for its transition from an ordered crystalline to a more fluid state. depends on acyl chain unsaturation and length

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51
Q

how does the transition temperature differ for artificial membranes vs biological membranes

A

transition temperature may be very sharp for artificial membranes because of homogenous preparation. not as sharp for biological membranes because of the mixture of different compounds and because the membranes have to function above the gel level but not be completely disordered

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52
Q

how does lipid composition in a biological membrane change with temperature?

A

with decrease temperature, more unsaturated fatty acids and shorter chains are incorporated into the lipids (because they have lower mp). with increasing temp more saturated fatty acids and longer chains are incorporated

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53
Q

how does cholesterol work at high temperatures

A

decreases disorder of acyl chains, increases rigidity and decreases fluidity

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54
Q

how does cholesterol work at low temperatures?

A

prevents close packing of acyl chains, decreases rigidity and increases fluidity

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55
Q

how do lipids move and dont move in the lipid bilayer?

A

only laterally, do not undergo transverse diffusion (flip flop) at appreciable rates because of energy barrier

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56
Q

how is transverse diffusion increased?

A

flipases increase the rate of transverse diffusion

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57
Q

what are the three types of membrane proteins?

A

integral membrane proteins, peripheral membrane proteins, lipid linked proteins

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58
Q

portion of integral membrane protein that is in contact with the acyl tails of the bilayer must have what?

A

must have hydrophobic amino acid side chains on its surface

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59
Q

how does the fluid mosaic model describe the membrane?

A

dynamic, non covalent, complex assembly of lipids and proteins

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60
Q

what types of molecules can cross the lipid bilayer by simple diffusion?

A

small non polar molecules

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61
Q

what does the rate of simple diffusion depend on?

A

size of molecule, concentration gradient, lipid solubility

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62
Q

what are the two major types of transport across biological membranes and what are their delta G’s?

A

passive transport, has a -deltaG, motion is spontaneous. active transport has +deltaG, energy must be provided to make transport occur

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63
Q

what do transport proteins do?

A

reduce the activation energy barrier for transport

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64
Q

what are two types of transport proteins for passive transport?

A

porins and ion channels

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65
Q

what is the structure of porins, and how are they in terms of selectivity?

A

porins are non selective, are trimers, with each subunit containing a water filled pore in the centre of a beta barrel

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66
Q

how are ion channels formed and how are they in terms of selectivity? what is this selectivity created by? explain why sodium ions cant pass through potassium channels

A

ion channels are formed between subunits, and are highly selective. selectivity depends on size and also the properties of the side chains/functional groups found. sodium is smaller than K+, but cant interact with the channel so it cant pass

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67
Q

transporter proteins

A

do not have membrane-spanning pores. conformational change alternates openings from one side of the membrane to the other. selective for substrate transported. may be passive or active

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68
Q

what are the three ways transporter (carrier) proteins are classified?

A

uniport (one molecule transported), symport (2 in the same direction), or antiport (2 in different direction)

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69
Q

what are the two types of active transport and how do they differ?

A

primary and secondary. primary typically uses ATP at the source of free energy. secondary uses ion gradient as the source of free energy

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70
Q

what is the Na+K+ ATPase an example of?

A

primary active transporter, activity of the pump is determined by the size of the concentration gradient

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71
Q

what is the Na+ glucose transporter an example of?

A

secondary active transport. symport

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72
Q

what are the chemical intermediates in metabolism called?

A

metabolites or metabolic intermediates

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73
Q

what do all pathways share?

A

same fundamental chemical and thermodynamic principes

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74
Q

what are the two major purposes of metabolism?

A

to obtain usable chemical energy from the environment, and to make the specific molecules that cells need to live and grow

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75
Q

anabolic pathways

A

use energy to build larger molecules and are generally reductive (electrons are used to make new bonds)

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76
Q

catabolic pathways

A

release energy (some of which is stored) and are generally oxidative (electrons are removed as bonds are broken)

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77
Q

amphibolic pathways

A

operate in both catabolic and anabolic processes

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78
Q

what are the most significant fuel sourcces

A

polysaccharides (complex carbohydrates), and triacylglycerol (fat)

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79
Q

what happens to excess fuels?

A

they are stored

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80
Q

what are carbohydrates stored as and where?

A

carbohydrates are stored as glycogen in the liver (heatocytes) and skeletal muscles (myocytes)

81
Q

what are fatty acids stored as and where?

A

stored as fats (triacylglycerols) in adipocytes

82
Q

what does actual free energy depend on? is it the same as standard?

A

actual free energy change depends on concentration of substances in system. not the same as standard, but are related

83
Q

what is the biochemical standard for the concentration of water?

A

55M

84
Q

what does deltaG > 0 mean?

A

reaction will not occur (in the forward direction)

85
Q

what does deltaG less than 0 mean

A

reaction will occur (spont/exergonic)

86
Q

what does deltaG way less than 0 mean

A

reaction can be considered “irreversible”

87
Q

what does deltaG approx 0 mean?

A

reaction is considered “reversible”. near equilibrium. changes in concentration of reactants or products may change the direction of the reaction

88
Q

what does it mean to say metabolic pathways exist in a steady state?

A

individual isnt changing, but overall is flowing. concentration of metabolic intermediates often do not change significantly once a pathway begins to operate

89
Q

what are high energy intermediates?

A

compounds with contain “usable” chemical energy, reactions associated with high deltaG

90
Q

what are three major types of high energy intermediates?

A

electron carries (NADH, NADPH, FADH2, FMNH2), nucleotide triphosphates (NTPS: ATP, GTP, UTP), thioesters

91
Q

what happens to cofactors in catabolism?

A

in catabolism, metabolites are oxidized, cofactors are reduced. usually NAD+ and FAD. reoxidization of the cofactors is used to generate ATP

92
Q

what happens to cofactors in anabolism?

A

metabolites are reduced, cofactors are oxidized. typically NADH

93
Q

what does the nitrogen base portion of NAD+ and FAD allow?

A

enables them to undergo a reversible reduction reaction

94
Q

what are NAD+ and NADP+ often involved in?

A

oxidation of C-O bonds ex oh to carbonyl

95
Q

what is FAD often involved in?

A

oxidation of C-C bonds ex c-c to c=c

96
Q

what can NAD+ and NADP+ be classified as in comparison to FAD/FADH2?

A

NAD+ and NADP+ are cosubstrates and FAD is a prosthetic group

97
Q

what does it mean that FAD/FADH2 is a prosthetic group? what does this in the CAC?

A

FADH2 must be reoxidized back to FAD for the next enzyme cycle to occur. in the citric acid cycle, this is done by coenzyme Q

98
Q

what is atp often called? what kind of bonds does ATP have that make it high energy?

A

energy currency. because of phosphoanhydride bonds (POP)

99
Q

what is the deltaG for a phosphoanhydride bond?

A

-32Kj/mol for the hydrolysis of a phosphoanhydride bond

100
Q

Do GTP or GDP have phosphoanhydride bonds?

A

they both do. can be considered high energy molecules

101
Q

what are the three things ATP does that make it a “high energy compound”

A

can break ATP down to ADP + P. separating these charges leads to decreased electrostatic repulsion. Phosphate also has more resonance which makes it more stable. also solvation effects

102
Q

how are thioesters different than esters?

A

thioesters are high energy compounds, and have no electron delocalization (unlike esters)

103
Q

how is ATP generated?

A

by catabolism. directly through substrate level phosphorylation, indirectly through oxidative phosphorylation

104
Q

how are reactions coupled?

A

a reaction with an overall unfavourable free energy change (deltaG > 0) can occur when another favourable reaction (deltaG less than 0) occurs in concert. THE COMBINED REACTIONS HAVE TO HAVE AN OVERALL DELTAG OF LESS THAN 0 TO BE SPONT

105
Q

what is phosphate transfer potential?

A

free energie to hydrolyze phosphate-containing compounds

106
Q

what steps are regulated in metabolism? what steps arent?

A

irreversible steps are usually regulated, while reversible steps are not regulated

107
Q

what is the rate limiting step

A

the irreversible, regulated reaction that determines the over all rate. usually regulated earlier in the pathway

108
Q

what are two types of metabolic inhibition

A

product inhibition and feedback inhibition

109
Q

what is product inhibition

A

an enzyme is inhibited by the product of its reaction

110
Q

what is feedback inhibition

A

an enzyme is inhibited by a metabolite further down the pathway. not the direct product of the enzyme, but a product further down

111
Q

how at metabolic pathways activated? what is this called?

A

an enzyme may be activated by a metabolite upstream. called feed forward activation

112
Q

what is reciprocal regulation?

A

pathways are regulated to ensure that both do not operate simultaneously

113
Q

what are two purposes the catabolic pathway serves?

A

breakdown of larger molecules into smaller building units , and release and temporary storage of energy in high energy molecules

114
Q

what are the two processes of oxidative phosphorylation and how are they linked?

A

they are two separate but connected processes. oxidation of reduced cofactors (NADH, FADH2), and phosphorylation of ADP to ATP. they are linked through a proton gradient across the mitochondrial membrane

115
Q

where does oxidative phosphorylation happen? what is the proton concentration difference between these two areas?

A

inner mitochondrial membrane. matrix has a high ph and low proton concentration, and the intermembrane space of the mitochondria has low ph and high proton concentration

116
Q

what are complexes I-IV in the electron transport chain?

A

integral membrane proteins

117
Q

where is coenzyme Q in the electron transport chain

A

it is inside the inner mitochondrial membrane because it is hydrophobic and lipid soluble. can freely move in lipid bilayer due to its tail

118
Q

where is cyctochrome c

A

it is a peripheral membrane protein

119
Q

how do electrons move in the electron transport chain?

A

electrons move from cofactors with low reduction potential to those with higher reduction potential

120
Q

what are some cofactors in the electron transport chain and what happens to them?

A

they are reversibly oxidized/reduced during electron transport. Flavin, iron-sulfur clusters, copper, cytochrome heme groups and coenzyme q

121
Q

what is flavin mononucleotide (FMN)

A

similar to FAD/FADH2 but no adenosine

122
Q

what are cytochromes?

A

hemoproteins that carry out electron transport

123
Q

what is the function of coenzyme Q?

A

transports electrons to complex III from complexes I and II in the inner mitochondrial membrane

124
Q

what does reduction potential mean? what does a higher reduction potential correspond to?

A

affinity for electrons. more negative deltaG

125
Q

what is the free energy changes from redox reactions used for?

A

used to transport protons across the membrane (primary active transport)

126
Q

what is oxygen used for in the electron transport chain and why?

A

used as the terminal electron acceptor because it has a very high reduction potential

127
Q

for every NADH reoxidized, how many protons are moved out of the matrix?

A

10 protons

128
Q

what does electron transport in the ETC that allows complexes to pump h+ ions?

A

electron transport causes a conformational change in these membrane complexes

129
Q

what is complex II called, what is it a part of, what is its function and how does it accomplish this function? how many protons are moved across the membrane by complex II?

A

succinate dehydrogenase, part of the CAC, funtion is to catalyze oxidation of succinate to fumarate and it contains prosthetic group FAD to do this. no protons are moved across the membrane at complex II

130
Q

for every FADH2 reoxidized, how many protons are moved out of the matrix? what complex is it associated with?

A

6 protons (note these protons arent being moved out of complex ii). FAD is a prosthetic group part of complex II.

131
Q

overall, what happens to the potential energy of the H+ gradient?

A

potential energy of the H+ gradient is converted to the chemical energy in the phosphoanhydride bonds of ATP

132
Q

is ATPsynthase part of the electron transport chain? what kind of transporter is it?

A

it is not, but its part of oxidative phosphorylation. it is a primary active transporter

133
Q

how many protons are needed per ATP synthesized through ATP synthase?

A

approximately 3H+ are needed for every ATP synthesized

134
Q

what are the two portions of ATP synthase?

A

the Fo portion and the F1 portion

135
Q

what does the Fo portion do? what is it inhibited by?

A

it is the transmembrane portion, protons pass through, triggers conformational change in F1. it is inhibited by oligomycin.

136
Q

what does the F1 portion do?

A

it is the catalytic portion, synthesizes ATP from ADP and P

137
Q

what determines the proton movement and ultimately oxygen consumption? why?

A

rate of ATP synthesize determines proton movement. this is because if the mechanism is not producing ATP, the protons will not move through the Fo portion of ATPsynthase

138
Q

what does oxidation do and what does phosphorylation do?

A

oxidation creates the H+ gradient, phosphorylation uses the H+ gradient

139
Q

how many active sites are there on ATP synthase and what is every turn of the shaft associated with?

A

there are 3 active sites at different stages, and every complete turn of the central shaft is associated with the generation of 3 ATP

140
Q

what does adenine nucleotide translocase do? what does it cause in terms of net charge?

A

exchanges newly synthesized mitochondrial ATP and cytosolic ADP, so it can be used to drive the many energy requiring processes in the cell. exchange of ADP and ATP causes the loss of a net charge of -1 in the matrix (ATP has a larger neg charge)

141
Q

how is phosphate brought into the mitochondria for the formation of ATP from ADP and P?

A

phosphate is transported in symport with H+. based on the concentration difference of H.

142
Q

what two transporters are needed for ATP formation? what is the combined energy loss and of transporting ATP out, and ADP and P in? what does this mean about the net protons needed for synthesis of one molecule of ATP?

A

the two transporters are the adenine nucleotide translocase and the phosphate-H symport. the combined energy loss is 1 H. the net protons you need for the synthesis of ATP is 4, 3 for ATP synthase and 1 to bring in a phosphate

143
Q

explain how oxidation and phosphorylation are coupled?

A

the rates of NADH reoxidation, of electron transport and oxygen consumption are coupled to the consumption of ATP through the magnitude of H+ electrochemical gradient.

144
Q

what is the P:O ratio?

A

the amount of ATP made per oxygen atom reducted to water

145
Q

what is the P:O ratio for NADH or FADH2? what are the non stero

A

NADH (10H moved across membrane / 4H needed per ATP)= 2.5, FADH (6H moved across membrane / 4H needed per ATP)=1.5

146
Q

what is the rate of oxidative phosphorylation determined largely by?

A

the relative concentration of ADP. ADP concentration reflects the energy consumption of the cell. when ADP concentration rises, oxygen consumption increases

147
Q

describe the coupling in oxidative phosphorylation when there is low energy use

A

Low energy use leads to low ADP concentration, which means there is low ATP synthase activity, the protons arent being used so the H+ concentration gradient increases, which decreases electron transport because you dont want to add to the gradient (leading to decrease o2 consumption) and NADH and FADH2 increase, which inhibits CAC and PDH

148
Q

describe the coupling in oxidative phosphorylation when there is high energy use

A

high energy use means that there is high ADP concentration (ATP is being used up), which means there is high ATP synthase activity, the proton gradient is decreasing, which increases electron transport to increase this gradient (o2 consumption increases), which decreases NADH and FADH2, which activates the CAC and PDH

149
Q

when is oxygen consumption increased in isolated mitochondria?

A

oxygen consumption is only increased when ATP synthesis is stimulated (addition of ADP)

150
Q

what happens to protons in uncoupled systems?

A

uncoupled systems allow protons to enter the matrix without ATP synthesis, generating heat instead of ATP

151
Q

what happens to oxygen consumption in the presence of an uncoupler?

A

oxygen consumption increases. the proton gradient is dissipated faster and so the rate of electron transport increases

152
Q

what is glycolysis?

A

conversion of 1 molecule of glucose into two molecules of pyruvate. generates ATP directly and NADH from oxidation of metabolites

153
Q

what kind of pathway is glycolysis?

A

anaerobic

154
Q

what are the two stages of glycolysis?

A

stage one: energy investment. stage 2: energy payout

155
Q

what is energy investment

A

glucose needs to be activated, ATP is consumed, involves hexose

156
Q

what is energy output

A

energy is harvested in the form of ATP, NADH is also generated, involves triose

157
Q

what reaction does hexokinase catalyze and is it irreversible or reversible? is it regulated?

A

hexokinase phosphorylates glucose to glucose-6-phosphate. it is irreversible. and regulated.

158
Q

what is the difference between glucose and fructose?

A

they are structural isomers . fructose is a ketohexose (6 carbon sugar containing a ketone)

159
Q

what reaction does pfk-1 catalyze? is it regulated?

A

pfk-1 catalyzes fructose-6-phosphate to fructose-1,6-biphosphate. it is regulated

160
Q

what is the rate limiting step in glycolysis?

A

fructose-6-phosphate to fructose-1,6-biphosphate catalyzed by pfk-1

161
Q

what is the oxidation step in glycolysis? what is it catalyzed by and what does it produce?

A

glyceraldehyde-3-phosphate to 1,3-BPG, catalyzed by glyceraldehyde 3-phosphate dehydrogenase. NADH is generated

162
Q

what is 1-3BPG considered?

A

a high energy intermediate because of its acyl phosphate

163
Q

why is glycolysis regulated?

A

ensures that energy needs are met, and that glucose is not wasted when ATP is abundant, and intermediates may be used elsewhere

164
Q

what is the rate of flux through metabolic pathways regulated by?

A

substrate availability, alteration of enzyme activity, alteration of amount of enzyme, and compartmentation

165
Q

what enzymes are regulated in glycolysis?

A

hexokinase, PFK1, and pyruvate kinase

166
Q

how is hexokinase regulated?

A

G6P is an inhibitor. acts as a negative allosteric effector. product inhibition

167
Q

how is PFK-1 regulated?

A

activated by ADP/AMP (concentration of ADP/AMP is a good indicator of a need for ATP in the cell). inhibited by PEP (elevated PEP levels show that pyruvate is not being used, no need for it)

168
Q

how is pyruvate kinase regulated?

A

ATP is an allosteric inhibitor (product inhibition), and activated by F-1,6-BP (feed forward inhibition)

169
Q

when is pyruvate kinase activated by F-1,6-BP?

A

in some tissue, and in yeast

170
Q

what are PFK-1 and PK both inhibited by? what is this called?

A

atp. synchronous regulation of irreversible reaction

171
Q

what is glycogen synthesized from? what does the breakdown of glycogen use? what does this do for the cell?

A

glucose-6-phosphate. uses inorganic phosphate to break glycosidic bonds. no ATP is used, which increases net yield of ATP for the cell and saves the cell energy (1 more per unit)

172
Q

why is an anaerobic fate for pyruvate required? explain. what are two types of anaerobic methods?

A

need to regenerate NAD+ for the oxidation step in glycolysis under anaerobic conditions, because usually NADH would be oxidized to NAD+ in the electron transport chain, but since anaerobic respiration doesnt have that, we use anaerobic methods like lactace production or ethanol production

173
Q

what kind of product is lactate in skeletal muscle?

A

it is a dead end product in anaerobic activity

174
Q

what happens to lactate in the muscle? why is this useful?

A

it is transported out via a specific membrane transporter protein. as lactace is being transported out, a proton is also transported out. according to the bohr effect, decreasing the ph in blood tissue protinates the groups associated with BPG, changing the confirmation to a T state. T state binds oxygen less, which leads to more oxygen released in the muscle. long story short, lactace increases o2 release in skeletal muscle

175
Q

what are the two ways NAD+ is regenerated for glycolysis to continue?

A

oxidative phosphorylation, and reduction of pyruvate (through lactate formation, or ethanol)

176
Q

what is lactate used for?

A

it is metabolic fuel for cardiac tissue

177
Q

where is the anaerobic production of ethanol?

A

not in vertebrates. happens in yeast

178
Q

what are the two steps of ethanol production? what are the final products?

A

decarboxylation and reduction. CO2, ethanol, NAD+

179
Q

what is the pyruvate dehydrogenase reaction and where does it occur? what is it catalyzed by?

A

concerts pyruvate to acetyl-coA. occurs in the matrix of the mitochondria. catalyzed by pyruvate dehydrogenase complex (PDH, PDC)

180
Q

where is pyruvate transport from, and where to?

A

glycolysis generates pyruvate in the cytosol, which must be transported to the matrix of the mitochondria to be converted to acetyl-coa

181
Q

what transporter protein moves pyruvate? what is transported with the pyruvate?

A

pyruvate translocase, symport with a proton

182
Q

what is the formation of acetyl-coA considered?

A

key irreversible step in carbohydrate metabolism

183
Q

what is the functional portion of acetyl-coa? what can it also appear as?

A

functional group is the terminal sulfhydryl (thiol). can also be thioester

184
Q

what is the pyruvate dehydrogenase reaction? what is it considered?

A

pyruvate + CoA + NAD+ -> acetylCoA + NADH + CO2. oxidative carboxylation

185
Q

describe the pyruvate dehydrogenase complex

A

multienzyme. 5 cofactors including NAD+, FAD, CoA.

186
Q

what is pyruvate dehydrogenase complex regulated by?

A

kinases and phosphatases

187
Q

what are advantages of having a multienzyme complex?

A

speeds up reactions, limits side reactions, enzyme controlled as a single unit

188
Q

where does the citric acid cycle occur?

A

in the mitochondrial matrix

189
Q

what does the cac generate?

A

oxidizes acetyl coa to co2. generates high energy products

190
Q

is the cac aerobic or anaerobic?

A

aerobic. O2 reduction to reoxidize NADH, FADH2

191
Q

where is QH2 reoxidized?

A

in the electron transport chain

192
Q

what is the rate limiting reaction in the CAC?

A

there is none, it is cyclic

193
Q

what are the inhibitors of the CAC? what are activators?

A

inhibitors are ATP, NADH. activators are ADP, Ca

194
Q

what is an anapleurotic reaction? what is an example?

A

replenishes the intermediates for the CAC. pyruvate carboxylase is an example.

195
Q

what catalyzes the formation of oxaloacetate. what is it activated and inhibited by?

A

reaction is catalyzed by pyruvate carboxylase. inhibited by ADP, activated by aceytl-Coa

196
Q

how many ATP’s does the CAC produce for each acetyl coa?

A

approx 10 atp

197
Q

how much atp does complete aerobic oxidation of glucose yield? what about anaerobic glycolysis?

A

32 vs 2

198
Q
A

phosphoanhydride bonds

biochem 200 (4 decks)

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