Biochemistry UIOWA Exam 3

How is carbon coming from glycolysis introduced into the citric acid cycle?

Pyruvate, the product of Glycolysis, is converted to Acetyl CoA by Pyruvate Dehydrogenase, which is the fuel for the CAC. irreversible

How does the compartmentalization of glycolysis and the citric acid cycle affect the pathways

Pyruvate has to be moved across the mitochondrial membrane, in the mitochondrial matrix it is converted to Acetyl CoA

What is the role of pyruvate dehydrogenase?

It decarboxylates pyruvate, creating CO2, NADH, and acetyl-CoA, It also does oxidative decarboxylation and NADH, ATP, and FADH2 are generated

What are the cofactors involved with pyruvate dehydrogenase?

Three catalytic coenzymes: TPP, Lipoic Acid, and FAD

Two sociometric coenzymes: CoA, NAD+

What are the three components of the pyruvate dehydrogenase complex?

E1: pyruvate dehydrogenase

E2: Dihydrolipoyl transacetylase

E3: Dihydrolipoyl dehydrogenase

Acetyl CoA

Pyruvate

Co-Enzyme A (CoA)

Effects of kinase on pyruvate dehydrogenase

Phosphorylates and inactivates E1

Effects of phosphatase on pyruvate dehydrogenase

Removes phosphate and activates complex

Effect of ATP, Acetyl CoA and NADH on pyruvate dehydrogenase

Inhibits

Effect of ADP and pyruvate on pyruvate dehydrogenase

stimulates

Citric Acid Cycle

oxidizes the acetyl fragment of acetyl-CoA to CO2, produces three NADH, one FADH2 and one ATP

What is the entry point reaction for Acetyl-CoA into the citric acid cycle

The condensation of the acetyl group with oxaloacetate (4 carbon compound) resulting in citrate (6 carbons)

Isocitrate synthase

Stage 1 of the citric acid cycle

formation of citrate and the two time oxidative decarboxylation of this 6 carbon compound to a four carbon compound Succinyl CoA produces 2 CO2 and 2 NADH

Stage 2 of the citric acid cycle

Regeneration of oxaloacetate; requires ADP and produces ATP, CoA, FADH2 and NADH

Regulation of isocitrate synthase

inhibited by NADH, succinyl-CoA, citrate, ATP (products)

regulation of isocitrate dehydrogenase

Activated by ADP

Inhibited by NADH and ATP

Regulation of a-ketoglutarate dehydrogenase

rate limiting step: inhibited by succinyl CoA, NADH, ATP

How does the Glyoxylate Cycle influence Glucose metabolism?

Enables plants and bacteria to convert fats into carbohydrates

loses reducing power

Where does the citric acid cycle occur?

The mitochondrial matrix

How is the compartmentalization of different steps in oxidative phosphorylation achieved?

Mitochondria contains an outer membrane, inner membrane and matrix. Not even protons can pass through the inner membrane. The electron transport chain gives energy to pump protons across the inner membrane from the matrix to the inner membrane

Oxidative phosphorylation in the electron transport chain

The flow of electrons from NADH and FADH2 to O2

Redox potential

The tendency of a member of a redox pair to donate or accept electrons. It is increased in the electron transport chain by the flow of electrons to oxygen

How does the transfer of electrons along the electron transfer chain generate ATP?

It forms a proton gradient which powers the creation of ATP by ATP synthase. The purpose of the electron transport chain is to generate a proton gradient.

What determines the sequence of complexes used for electron transfer?

The redox potential, members of the electron transport chain are arranged so that electrons always flow ro components with more-positive electron reduction potentials (higher e- affinity)

Coenzyme Q (ubiquinone)

Carrier it transfers electrons from both complex 1 and 2 to complex 3

NADH oxidoreductase

Complex 1: Entrance of NADH, flow of 2 electrons pumps 4 protons from matrix to intermembrane space

Coenzyme Q-Cytochrome C oxidoreductase

Complex 3: catalyzes the transfer of electrons from QH2 to cytochrome c, 2 protons pumped into the intermembrane space.

cytochrome C reductase

Complex 4: catalyzes the transfer of electrons from reduced cytochrome c to oxygen. 8 protons removed, 2 H2O and 4 protons pumped into intermembrane space.

Role of O2 in the electron transport chain

terminal electron acceptor

How is toxicity from oxygen radicals mitigated?

superoxide dismutase and catalase help protect against ROS

Complex 2

non-transmembrane

How is a proton gradient converted to ATP?

ATP synthase, protons flow through a proton chanel powering ATP synthase. Formed from ADP and orthophosphate

sequence of events that happen during ATP synthesis

3 active sites, C ring rotates gamma subunit which interconverts B-subunits

ATP synthase B subunit loose conformation

binds ADP and Pi

ATP synthase B subunit T conformation

binds ATP, converts ADP and Pi

ATP synthase B subunit O (open) form

Releases ATP

Where is ATP generate?

ATP synthase within the inner mitochondrial membrane

How is ATP redistributed?

ATP-ADP translocase, coupled transport of ATP out and ADP in (antiporter)

How many ATP formed from the complete combustion of glucose?

30, 26 via oxidative phosphorylation

Glycerol 3-phosphate shuttle

Allows electrons from the cytoplasm to enter the electron transport chain

malate-aspartate shuttle

NADH from cytoplasm to the mitochondria in the heart and liver.

mitochondrial uncoupling

any process by which the electron transport chain is not used to drive ATP synthesis or other useful work such as net ion translocation, regulated uncoupling: brown fat

Regulation of the rate of oxidative phosphorylation

Rising levels of ADP speed up oxidative phosphorylation

What poisons affect oxidative phosphorylation?

Inhibitors and uncouplers,

What are the products of the light reactions

Converts light to chemical energy

General product of photosystem 1

reducing power NADPH, O2

General product of photosystem 2

Proton gradient

Calvin cycle

reduce CO2 to produce glucose

Where does photosynthesis occur?

Chloroplast

What are the three types of membrane in chloroplasts

Outer, inner, thylakoid

What are the three spaces within chloroplasts

Intermembrane space, stroma, lumen: interior of thylakoid

Thylakoid membrane

Redox reactions,

Which processes transfer energy from excited electrons?

Light creates a separation of charge which induces electron flow. Redox

How to antenna chlorophylls and other pigments contribute to light harvesting?

Use resonance energy transfer to transfer energy to the reaction center

Where does photosystem 1 transfer electrons

From H2O to NADPH

Where does photosystem 2 transfer electrons

Provides electrons to photosystem 1

How is the proton gradient produced by photosystem 2?

The cytochrome complex transfers electrons from plastoquinone (Q) to plastocyanin, pumps protons

Manganese center in photosystem 2

water oxidizing complex

Role of ferredoxin in photosynthesis

transfers electrons to NADP+ then NADPH

Cytochrome b6f complex

bridge for PS1 and PS2, QH2 enters is and loses its electrons to reduce plastocyanin. protons are pumped across the membrane to produce proton gradient.

Plastoquinone (Q)

Similar to Coenzyme Q (ubiquinone). carrier of electrons to cytochrome complex

Plastocyanin

receives electrons in the cytochrome complex, provides them to PS1

Regulation of the light reactions

cyclic photophosphorylation: electrons redirected from photosystem 1 to cytochrome b6f complex. no production of O2 and NADPH.

Calvin Cycle

Fixes carbon dioxide into sugar, using energy from the light reactions, draws CO2 from the air

Fixation stage of the calvin cycle

Enzyme called Rubisco catalyzes reaction between ribulose 1,5-bisphosphate and CO2, producing two 3C molecules

Reduction stage of the calvin cycle

two 3-phosphoglycerides are reduced to make fructose 6 phosphate, requires 2 ATP and 2 NADPH

Regeneration stage of calvin cycle

regenerates ribulose 1,5-bisphosphate, requires ATP

Rubisco (enzyme)

Rate limiting step of calvin cycle, bound CO2 forms a carbamate with lysine 201

What are the starting products of the regeneration step in the calvin cycle

Hexose monophosphate pool, G1P, G6P, F6P

Stoichiometry of Calvin Cycle

6 cycles are required to make one 6 C glucose, 12 ATP total (2 percycle)

Starch

glucose polymer with a-1,4 and a-1,6 linkages

Sucrose

disaccharide of glucose and fructose

Regulation of the calvin cycle by light reactions

Rubisco is activated by light, conditions change to support the calvin cycle when given light

Regulation of the calvin cycle by thioredoxin

High levels of thioredoxin activate the enzymes in the calvin cycle

Photorespiration

Rubisco reacting with O2 with no fixation, requires 1 more ATP and releases ATP,

What is the structure of glycogen?

Polymer of glucose with a-1,4 linkages to form linear arrays and a-1,6 linkages to form branches (1 in 12)

Glycogen Degradation: glycogen phosphorylase

Activity 1: cleaves the glucose ends of glycogen chains (regulated and committed step)

Glycogen Degradation: glycogen phosphorylase b

less active non phosphorylated , T state.

Glycogen Degradation: glycogen phosphorylase a

more active, phosphorylated, R state.

What is the regulated and committed step of glycogen degradation?

The cleavage of the glucose ends of glycogen chains by glycogen phosphorylase.

Glycogen Degradation: Transferase

Activity 2: moves 3 glucose residues to another chain

Glycogen Degradation: a-1,6-glucosidase (debranching enzyme)

Activity 3: hydrolyses a-1,6 linkages

Glycogen Degradation: Hexokinase

Activity 4: Phosphorylates glucose released by debranching enzyme

Glycogen Degradation: Phosphoglucomutase

Activity 5: converts G1P to G6P

Glycogen Degradation: Glucose 6-phosphatase

Activity 6: dephosphorylates G6P in liver to allow transport into blood

glycogen phosphorylase regulation in muscles

Regulated by energy status

glycogen phosphorylase regulation in the liver

default is active unless free glucose is present

What is the role of UDP in glycogen synthesis?

It is the substrate for polymerization via a-1,4 linkages catalyzed by glycogen synthase

Glycogen synthesis: Glycogen synthase

catalyses the synthesis of glycogen, only forms a-1,4 linkages, regulatory enzyme

Glycogen synthesis: Branching enzyme

Breaks a-1,4 linkages and forms a-1,6 bonds

UDP-glucose pyrophosphorylase

catalyses the synthesis of UDP-glucose

What is the energy cost of glycogen synthesis

2 ATP

effects of epinephrine of glycogen synthesis and degradation

epinephrine activates degradation and deactivates synthesis, need more energy!

Protein phosphatase 1 (PP1)

Accelerates glycogen synthesis and decelerates glycogen breakdown, dephosphorylate glycogen synthase stimulating enzyme

Insulin

When blood glucose is high, insulin stimulates the synthesis of glycogen

Diabetes Type 1

caused by autoimmune destruction of beta cells in pancreas that make insulin

Diabetes Type 2

Body stops responding to insulin

McArdle's disease

cannot proper mobilize stored glycogen, extended exercise, myophosphorylase