Biochemistry 305 Final

Front 1

Amphibolic pathway

Back 1

A metabolic pathway that functions in both catabolism and anabolism. This is what glycolysis is.

Front 2

Glycolysis summery reaction

Back 2

2 pyruvates are generated from one hexose (glucose) molecule. The reaction also makes 2 NADH's and 2 ATP's (4 made and 2 are used)

Front 3

Glycolysis Step 1

Back 3

This is the energy priming (investment) step. Glucose is phosphorylated twice. This is done to lock it into the cell so that it can't diffuse away

Reaction: glucose--glucose-6P---fructose-6P----fructose-1,6P---dihydroxyacetone-P and Glyceraldehyde-3P

Phosphofructokinase is the enzyme that catalyzes fructose-6P to fructose-1,6P

Front 4

Glycolysis step 2

Back 4

This is the energy payoff step. Here G-3P is converted to pyruvate. 2 NADH and 2 ATP are made. This is subsrate-level phosphorylation (conserving covalent bonds).

Front 5

Three Possible fates of Glycolytic Pyruvate

Back 5

1. It goes on to TCA cycle to make ATP and NADH when oxygen is present

2. Lactic Acid Fermentation when oxygen is absent

3. Alcoholic Fermentation (ethanol made) when oxygen absent

Front 6

Lactic Acid Fermentation

Back 6

Lactate Deyhrdogenase converts pyruvate to lactate using NADH. This regenerates NAD+ that can be used in glycolysis so that some ATP can be made. This occurs in over exercised muscles.

Front 7

Alcohol Fermentation

Back 7

This is a 2 step process where pyruvate is converted to ethanol. In the first step pyruvate decarboxylase converts pyruvate to acetaldehyde. Alcohol dehydrogenase then converts that to ethanol.

Ethanol consumption stimulates the synthesis of NADH using the reverse of this reaction. The excess NADH can inhibit glycolysis and fatty acid oxidation. The accumulation of fatty acids in the liver can cause cirrhosis.

Front 8

What is Energy Charge?

Back 8

A mathematical expression that relates or describes the relative availability of metabolic energy in terms of the amounts of ATP and ADP/AMP. High energy charge means high availability of ATP.

Look up the expression and memorize it.

Muscle: 0.7-0.99
Blood: 0.4-0.98

Front 9

Overview of the TCA cycle

Back 9

This is the complete oxidation of pyruvate to carbon dioxide. It also produces NADH FADH2 and ATP. OAA is regenerated at the end of the cycle.

Front 10

Anaplurotic pathway

Back 10

Pathway where the starting material is reproduced (krebs).

Front 11

Enzymes of the TCA Cycle in Order

Back 11

1. pyruvate dehydrogenase 2. citrate synthase 3. Aconintase 4. isocitrate dehydrogenase 5. a-ketoglutarate dehydrogenase 6. succinyl-CoA synthase 7. Succinate dehydrogenase 8. furmase 9. malate dehydrogenase

Regulatory enzymes (1,2,4,5) are all irreversible.

Front 12

Pyruvate Dehydrogenase

Back 12

A complex of 3 enzymes. It promotes the entry of pyruvate into the cycle via the formation of acetyl-CoA. It is technically not part of the TCA.

Front 13

Pyruvate Dehydrogenase Complex Components

Back 13

E1: "Pyruvate Dehydrogenase"- functions to decarboxylate pyruvate

E2: Dihydrolipoyl transacetylase: functions to transfer the acetyl group from pyruvate to CoASH

E3: Dihydrolipoyl Dehydrogenase- functions to reoxidize dihydrolipoamide by making NADH from NAD

There is also a kinase attached to the complex that will inactivate it when ATP present

Front 14

Regulation of Pyruvate Dehydrogenase

Back 14

ATP, acetyl CoA and NADH inhibit
AMP, CoASH, and NAD activate

For the kinase
pyruvate, CoASH, and NAD inhibit
ATP, acetyl CoA, and NADH activate (opposite of above)

Front 15

Citrate Synthase

Back 15

Allows entry of acetyl units via condensation of OAA to form citrate (OAA + acetyl-CoA).

Inhibitors: NADH, ATP, and citrate
Activators: NAD, ADP, acetyl-CoA, and OAA

Front 16

Isocitrate Dehydrogenase

Back 16

Oxidation of isocitrate to a-ketoglutarate where NADH and carbon dioxide are made.

Inhibit: ATP, NADH, and succinyl-CoA
Activate: ADP and NAD

Front 17

a-Ketoglutarate Dehyrdrogenase

Back 17

Oxidation of a-Ketoglutarate to succinyl-CoA where NADH and CO2 are released.

Inhibit: Succinyl-CoA and NADH inhibit

Front 18

Succinyl-CoA Thiokinase (synthase)

Back 18

CoA thioester is cleaved to form succinate. There is substrate level phosphorylater wher GTP is created. Nucleoside diphosphate kinase converts the GTP to ATP.

Front 19

Succinate Dehydrogenase (important)

Back 19

This is also part of the ETC. The enzyme is located in the cristae membrane.
Succinate is oxidized to furmate, which makes a trans double bond.

Inhibit: OAA
Activate: *ATP*, and P

Front 20

Malate Dehydrogenase

Back 20

This is the final and anaplerotic reaction of the TCA. Malate is oxidized to "regenerate OAA." NADH is also produced.

The change in G for the reaction is high so it doesn't happen spontaneously. It is pulled forward by the depletion of OAA.

Front 21

Total Nucleotides of TCA

Back 21

there are 12 total nucleotides produced. 10 are NADH and 2 are FADH2.

Glycolysis and TCA will stop if nucleotides are not regenerated though.

Front 22

4 membrane complexes of the ETC

Back 22

complex I: NADH dehydrogenase

complex II: Succinate dehydrogenase

complex III: Cytochrome b/c1 complex

complex IV: cytochrome c oxidase

Front 23

Flavoproteins

Back 23

FAD, FMN
effect single or double electron and H+ transfers

Front 24

Fe-S proteins

Back 24

2-4 Fe's bounds to protein via cysteine residues

single electron transfers

Front 25

Cytochromes

Back 25

Heme proteins

carry single electron

Front 26

Ubiquinone (coenzyme Q)

Back 26

lipophilic molecule in the membranes

carries 2 electrons and 2 H+'s

Front 27

ETC complex I

Back 27

NADH gives its electron to NADH dehydrogenase. The e flows through 2 Fe-S proteins and a bound CoQ.
It eventually goes to UQ to form UBH2
Every NADH makes 4 H+s go to the intermembrane space.

Front 28

ETC complex II

Back 28

Here FAD gives e's directly to UQ after it reaches succinate dehydrogenase

or

NADH from glycolysis gives its e's to FAD, which then gives it straight to UQ.

Front 29

ETC complex III

Back 29

Cytochrome c accpects the e's from UQ at the cytochrome c complex. However, the H+s from UQH2 are not accepted, so they go to the intermembrane space.

Front 30

ETC complex IV

Back 30

Here cytochrome c gives its e's to make water. For every 4 cytochrome c's that go through, 4 H+s go to the intermembrane space.

There is also an ATP binding site that inactivates it when ATP is high.

Front 31

Amounts of H+'s moved in each ETC step

Back 31

1 NADH has 2 e's, which will move 10H+s to the intermembrane space. 8 come from krebs giving 80 total

2 NADH's come from glycolysis and enter at complex 2 to move 6 H+'s each for a total of 12.

2 FADH2 come from the krebs cycle which move 6 H+s each as they enter at complex 2 for a total of 12.

104 H+'s are move to the intermembrane space for every 1 hexose brokendown.

Front 32

Rotenone (ETC)

Back 32

Poison that is used as a pesticide by farmers but can also poison nearby fish. It stops ECT at complex I

Front 33

Amytal (ETC)

Back 33

Used as a sedative for horses because it stops complex I. This means no e's come from the TCA, but some still come from glycolysis.

Front 34

Antimycin (ETC)

Back 34

poison used to treat wounds

Front 35

Cyanide (ETC)

Back 35

blocks the end of ETC and kills you. Prevents e's from being accepted by oxygen. Also happens with CO.

Front 36

Oxidative phosphorylation

Back 36

ATP synthesis coupled to oxidative processes of respiratory electron transport

Front 37

Chemi-Osmotic Coupling Theory

Back 37

Proposed by Mitchell
Said that chemical reations (atp synthesis) could be coupled to osmotic gradients

Front 38

Postulates of the Chemiosmotic Theory

Back 38

energy derived from electron transport is temporarily stored as a transmembrane charge difference and pH.

Protons can pass back through the membrane through ATP synthase.

The return is coupled by ATP synthesis

Front 39

Uncouplers

Back 39

hydrophobic compounds with a dissociable proton carry protons back across the membrane

Front 40

Ionophores

Back 40

hydrophobic molecules that insert into membranes to form channels that allow the free passage of cations back across the membranes

Front 41

Types of uncouplers of ATP synthesis

Back 41

Dinitrophenol- toxic phenol, used as an insecticide, humans are toxic reaction including fatigue, elevated body temperature, and cyanosis
Gramicidin- antibiotic produced by Bacillus breva, used to treat local infection of gram+ bacteria

Front 42

Heat generation by uncoupled mitochondria

Back 42

important in hibernating and cold adapted animals and newborn infants

The uncoupler thermogenin is activated by fatty acids of adipose cells

Front 43

ATP Synthase Structure

Back 43

The two main complexes are the transmembrane stalk and the sphere
Subunits:
A -regulatory
beta and delta- hold the sphere in place and keep it from rotating
gamma- drive shaft of the rotation
epsilon-part of the rotor but function is unknown
C functions as the rotor

Front 44

The Binding Change Mechanism for ATP Synthesis

Back 44

The rotor of ATP synthesis has 3 distinct active sites: open, loose, and tight
The open site is where ADP and P are not bound and are allowed to enter
The loose site is where ADP and P come together
The tight site is where ADP and P are brought close enough together to cause a bound to form to create ATP

Front 45

Glycerol-3-Phosphate Shuttle

Back 45

This occurs in the brain and skeletal muscles
NADH can't enter the mitochondria.
The e's from NADH go to G3-P which then goes into the membrane to transfer the e's to FADH2. These e's can then go to complex II of the ETC

Front 46

The aspartate-malate shuttle

Back 46

This occurs in liver cells where NADH can't enter the membrane of the mitochondria.
First, aspartate is converted to OAA. The e's from NADH then go to OAA and convert it to malate. The malate can then enter the membrane and recreate NADH as it changes back to OAA.

Front 47

Amount of ATP from every step of Respiration

Back 47

8 NADH-20 ATP
2 FADH2- 3 ATP
2 NADH from glycolysis- 3 ATP
SLP (from glycolysis and TCA)- 4 ATP

This gives 30 total for muscle and nerve cells, but liver cells have 32* ATP

Front 48

Location of Photosystems

Back 48

the light dependent reactions take place in the thylakoid membrane and function to create NADPH and ATP
The light independent reactions take place in the stroma of the chloroplast and function to create hexoses in the Clavin Cycle

Front 49

Overall Flow of Electrons in the Light Dependent Reactions

Back 49

Electrons are excited by the light on either the chlorophyll a or b molecules and come from water molecules. They move from photosystem II to the cytochrome b6 complex. They then move to photosystem I. After moving through this system, then finally go on to make NADPH.

All the processes release H+s to the thylakoid membrane to create a gradient used to generate ATP.

Front 50

The photosynthetic pigment structures

Back 50

chlorophyll a- long H-C chain with a magnesium containing group on one end with a CH3 group
chlorophyll b- long H-C chain with magnesium containing group and a CHO group
pheophytin- same structure as ch a but there is no magnesium
B-carotene- H-C chain with a ring on both ends and no groups
Xanthophylls- (Lutein) H-C chain with two rings on a each end and an OH group on one end

Front 51

Important Characteristics of the Photosynthetic Pigments

Back 51

Hydorphobic: they are embedded in the membrane and hydrophobic proteins
Conjugated Double Bonds- they have alternating double bonds on the chains that allow resonance. This allows the easy flow of e's and e's can energize easily

Front 52

The Action Spectrum of Photosynthesis

Back 52

Chlorophyll a can absorb blue and red light.
Chlorophyll b can absorb green/yellow and orange/red
Carotenoids can absorb purple to green light.
Plants filter out green and yellow light, giving them a green color.

Front 53

Three fates of Excited Electrons in Light Dependent Reactions

Back 53

1. The e's return to the ground state. In doing this they emit red light and heat (radiationless decay)

2. There is a resonance energy transfer. This is the exchange of a high energy electron for a low energy electron. However, there is no net gain or loss of e's

3. There is a net electron transfer. This occurs at the center pigments, from which the e's are then transferred to the primary acceptor. This is called photochemistry or energy transduction.

Front 54

What is a Photosynthetic Unit?

Back 54

It is the smallest group of pigment molecules and associated proteins and electrons capable of absorbing a photon of light and effecting the transfer of one electron.

Front 55

Components of PS I

Back 55

1. light harvesting complex I with pigments
2. P700 reaction center
3. A0- the primary acceptor of PS I
4. Q- Phylloquinone- another chl a acceptor
5. Fd- ferredoxin- a loosely attached group that transfers e's
6. FNR- ferredoxin NADP+ reductase- transfers e's from PS I to make NADPH

Front 56

Components of PS II

Back 56

1. light harvesting complex II with pigments
2. P680- reaction center
3. Pheo- primary acceptor
4. Qa and Qb- tightly and loosely bound plastoquinones
5. D1 and D2- proteins that hold Qa and Qb.
MSP- manganese stabilizing protein

Front 57

Phylloquinone (Q)

Back 57

electron carrier of PS I
It is also known as vitamin K1
It is a H-C chain with two rings on one side

Front 58

Plastocyanin

Back 58

It is a water soluble Cu-protein electron carrier.
It carries 1 e from Cyt b6/f complex to P700 of PS I

Front 59

Plastoquinone

Back 59

Electron carrier that is freely mobile in the membrane.
It carries 2 H+'s and 2 e's from PS II to Cyt b6/f complex.
The Cyt b6 complex only accepts e's so all of the H's are released into the thylakoid lumen (acts as a shuttle).

Front 60

The water oxidizing clock of PS II

Back 60

It functions to replace the e's lost at PS II reaction center (P680). This is done by disassembling water. Oxygen is released.
Also called the manganese stabilizing protein.

Front 61

Cyclic Electron Transport in Light Dependent Reactions

Back 61

This is when ferredoxin separates from PS I and goes back in the mechanism to reduce Qb. In this way the e's from Fd are not transferred to make NADPH, but are cycled. A H+ gradient is still made as the e's cycle, so ATP can be made, but not NADPH.

Front 62

Discovery of the Calvin Cycle

Back 62

The work was done by Calvin and Benson. They injected radioactive carbon dioxide into growing algae. Discovered C3 photosynthesis.

Front 63

The three phases of the Calvin Cycle

Back 63

1. Carbon fixation
2. Reduction Reactions
3. Regeneration Reactions

Front 64

Rubisco reaction

Back 64

The full name is ribulose-1,5-bisphosphate carboxylase.
1. ribulose-1,5-bisphosphate converts to a en-diol form
2. CO2 is added to it
3. water is added to it
4. the molecule is split to make 2 phosphoglyceraldhyde mole

Front 65

Rubisco Notes

Back 65

It is the most abundant protein in nature.
It is inefficient with turnover number of 2-3 Kcat
It is very complex with 16 subunits (8 large and 8 small).
The large subunits come from chloroplast DNA and the small subunits come from nuclear DNA.

Front 66

Reduction Reaction of the Calvin Cycle

Back 66

This is a two step mechanism. 2/3 of the ATP and all of the NADPH from the PSeT are consumed.
glyceraldehyde- 3-phosphate is made (gald-3P)

Front 67

Regeneration Reactions

Back 67

2 gald-3P's are exported from the chloroplast to form a hexose.
Ribulose -5P is phosphorylated by ribulose-5P kinase to regenerate the starting marerial, RuBP.
The last 1/3 of the ATP form PSeT is consumed.

Front 68

Modes of Light Mediated Calvin Cycle Enzyme Regulation

Back 68

1. changes in the stroma pH
2. changes in the stroma mg2+ concentration
3. reductive activation
4. allosteric regulation
5. carbamoylation

Front 69

Reductive Activation of the Calvin Cycle Enzymes

Back 69

Fd detatches from PS I and moves e's to thioredoxin.
This causes the thioredoxin to have a disulfide. It then transfers its e's to an inactive enzyme, making it develop a disulfide to activate it.

Front 70

Regulation of Rubisco

Back 70

1. Rubisco Activase uses ATP to activate rubisco by removing anything blocking the active site.
CA1P is made in the evening to compete for the active site and turn off rubisco. In the morning rubisco activase removes it

2. Carbamoylation can occur on the lysine of the acitve site in a reaction with CO2 to activate rubisco. This is only when the active site is empty and CO2 is high.

Front 71

Rubisco as an Oxygenase

Back 71

Rubisco can work as an oxygenase by mistake instead of a carboxylase sometimes.
20% of the time rubisco is an oxygenase and 80% of the time it is a carboxylase.
The oxygenase reaction creates 1 G3-P and aone phosphoglycerate molecule which must be recovered to be used in the Calvin Cycle.

Front 72

Salvaging of P-glycollate in Photorespiration

Back 72

The salvage reaction is only 75% effective.

This is the order of the reaction:
P-glycollate----glycine (peroxisomes)-----serine (mitochondria)-----glycerate (peroxisomes)-----3P-G (chloroplast)