Important Biochemistry Concepts

Question 1

Glycolysis, 3 major steps?

Answer 1

Hexokinase converts glucose to glucose-6-p (ATP cost)

Phosofructase(PFK) converts fructose-6-P to fructose-1,6-P2 (ATP cost) (COMMITTED STEP)

Pyruvate kinase converts PEP to pyruvate, produces 2 ATP

Question 2

Glycolysis, anaerobic or aerobic

Answer 2

Anaerobic

Question 3

Glycolysis, full chemical reaction?

Answer 3

Glucose -> Glucose-6-Phosphate -> Fructose-6-Phosphate -> Fructose-1,6-biphosphate (COMMITTED)

-> Glyceraldehyde-3-Phosphate-> 1,3-Bisphosphoglycerate -> 3-Phosphoglycerate -> 2-Phosphoglycerate -> PhosphoenolPyruvate -> Pyruvate

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Question 4

Glycolysis, overall reactants and products?

Answer 4

Reactants: Glucose, 2NAD+, and 2ADP,Pi

Products: 2 Pyruvate, 2NADH, and 2ATP, 2H+

Question 5

Glycolysis, location?

Answer 5

Cytosol

Question 6

Fermentation, purpose?

Answer 6

Oxidizes NADH to regenerate NAD+ while reducing pyruvate to lactic acid (or ethanol, yeast)

Question 7

Pyruvate dehydrogenase complex, definition?

Answer 7

Where oxidative decarboxylation of pyruvate occurs to regenerate acetyl-CoA

Question 8

Pyruvate dehydrogenase complex, location?

Answer 8

Mitochondrial matrix

Question 9

Pyruvate dehydrogenase complex, overall reactants and products?

Answer 9

Uses up CoA, NAD+, pyruvate

Creates NADH, CO₂, Acetyl-CoA

Question 10

Importance of thiamine

Answer 10

TPP is a prosethetic group that helps with decarboxylation of pyruvate, it is derived from Thiamine (Vitamin B)

Pyruvate Decarboxylation Complex

Question 11

Pyruvate dehydrogenase complex, allosteric inhibition?

Answer 11

ATP and fatty acids inhibit oxidative decarboxylation of pyruvate by the pyruvate dehydrogenase complex, s_ince acetyl-CoA goes to fatty acid and ATP synthesis_

Pyruvate dehydrogenase also creates NADH and Acetyl CoA, high levels of those inhibit the function

Question 12

Krebs Cycle, purpose?

Answer 12

Production of 3 NADH and 1 FADH2 for the electron transport chain

Also produces 2 ATP

Question 13

Krebs Cycle, location?

Answer 13

Mitochondrial Matrix

Question 14

Krebs Cycle, overall reactants and products?

Answer 14

Per 1 turn:

Reactants: Acetyl-CoA (from pyruvate), OAA from previous cycle

Products: 2 CO2, 3 NADH, 1 GTP, 1 FADH₂

each glycose does 2 turns

Question 15

Krebs Cycle, regulation methods?

Answer 15

Substrate availability - amino acids can be converted to alpha-ketoglutarate to speed up cycle

Substrates inhibit their enzymes - citrate inhibits citrate synthase; succinyl-CoA inhibits aKG dehydrogenase

Allosteric regulation - ATP, NADH inhibit TCA cycle

Question 16

Krebs Cycle, full chemical reaction?

Answer 16

-> Citrate -> Isocitrate -> alpha-Ketaglutorate -> Succinyl-CoA -> Succinate -> Fumarate -> L-Malate -> OAA -> Citrate

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Question 17

Kreb Cycle, steps that produce NADH?

Answer 17

Isocitrate dehydrogenase - Isocitrate to alpha-ketoglutarate

aKG dehydrogenase - alpha-keto glutarate to succinyl CoA

Malate dehydrogenase - malate to OAA

3 per turn, 6 per glucose

Pyruvate Dehydrogenase complex also produces an NADH

Question 18

Krebs Cycle, steps that produce FADH2

Answer 18

Succinate dehydrogenase - Succinate to fumarate

1 per turn, 2 per glucose

Question 19

Krebs Cycle, steps that produce GTP?

Answer 19

Succinyl-CoA synthetase - succinyl-CoA to succinate

Question 20

What is oxidative phosphorylation?

Answer 20

The electron transport chain (Empty electron carriers) + chemiosmosis (ATP production)

Question 21

Electron transport chain, location?

Answer 21

inner Mitochondrial Membrane. (Protons are pumped into the intermembrane space from the matrix)

Question 22

Electron transport chain, purpose?

Answer 22

To create a proton gradient as NADH and FADH2 are oxidized

Question 23

Electron transport chain, location?

Answer 23

Inner mitochondrial membrane

Question 24

Electron transport chain, pathway?

Answer 24

Complex 1 - NADH dehydrogenase enzyme, pumps hydrogen into intermembrane space and transfers electrons from NADH

Complex 2 - Succinate dehydrogenase enzyme, transfers electrons from FADH2, no H+ pumped

Ubinquinone (Q) - Transfers electrons from Complex 1 and 2 to Complex 3

Complex 3 - Cytochrome C reductase enzyme, carries electrons to complex 4, pumps protons into intermembrane space

Cytochrome C - Transfers electrons from Complex 3 to Complex 4

Complex 4 - Cytochrome C oxidase enzyme, oxygen is converted to water, pumps protons into intermembrane space

Onward to Chemiosmosis

Question 25

Electron transport chain, definition of prosthetic groups?

Answer 25

A prosthetic group is a non-protein molecule required for the activity of a protein

Question 26

Electron Transport chain, overall reactants and products?

Answer 26

Reactants: **Hydrogen ions, oxygen, NADH, FADH2** Products: **Water, ATP**

Question 27

ATP yield, value of NADH?

Answer 27

2.5 ATP

Question 28

ATP yield, value of FADH2?

Answer 28

1.5 ATP

Question 29

ATP yield, total eukaryotic and prokaryotic?

Answer 29

Eukaryotic = ~30 ATP Prokaryotic = ~ 32 ATP

Question 30

Gluconeogenesis, purpose?

Answer 30

Produces **glucose** from **pyruvate** with **ATP** when glucose is low (**fasting**) and ATP is high

Question 31

Gluconeogenesis, overall reactants and products?

Answer 31

Reactants: **4 ATP, 2 GTP, 2 NADH, 2 pyruvic acid,** 6H2O, 2H+ Products: **Glucose, 4 ADP, 2 GDP, 2 NAD+,** 6HPO4^2-, 6H+ (Reverse of Glycolysis)

Question 32

Gluconeogensis, location?

Answer 32

Mainly liver, also kidneys

Question 33

Gluconeogenesis, how does glucose production differ from glycolysis?

Answer 33

Irreversible Formation of glucose, fructose-6-P, and PEP are irreversible steps that push equilibrium to favor gluconeogenesis

Question 34

Gluconeogensis, what is the alternative mean of raising blood glucose levels?

Answer 34

Degradation of glycogen, stored in the liver

Question 35

Gluconeogenesis, pathway and important enzymes?

Answer 35

Reverse path of glycolysis, with alternatives for glycolysis's irreversible steps 1, 3 and 10. Alternative enzymes: _Pyruvate carboxylase_ to convert pyruvate to **OAA** _PEP carboxykinase_ to convert **OAA** to **PEP** *(OAA is unique intermediate, glycolysis has direct transition from pyruvate to PEP)* _Fructose-1,6-bisphosphatase_ to convert **Fructose-1,6-bisphosphate** to **Fructose-6-Phosphate** _Glucose-6-phosphatase_ to convert **Glucose-6-Phosphate** to **Glucose**

Question 36

Gluconeogenesis, enzymes that require ATP

Answer 36

_Pyruvate carboxylase_ (unique), pyruvate to OAA _PEP carboxykinase_ (unique), OAA to PEP _Phosphoglycerate kinase_ (also glycolysis), 3-phosphoglycerate to 1,3-bisphosphoglycerate 6 total per glucose *Steps 10(x2) and 7 of glycolysis, and steps 1 and 5 of gluconeogenesis)*

Question 37

Gluconeogenesis, steps that require NADH?

Answer 37

1,2-biphosphoglycerate to glyceraldehyde-3-P 2 total per glucose (Step 4 of glycolysis)

Question 38

Gluconeogenesis, possible starting material?

Answer 38

Lactate, pyruvate, glycerol (enters through dihydroxyacetone phosphate), amino acids (enters through pyruvate), any Krebs cycle intermediates (enters through OAA)

Question 39

Glycogenesis, purpose and regulation?

Answer 39

Production of **glycogen** from **glycose** to store in skeletal **muscle** and/or **liver** Stimulated by **insulin** and **high glucose levels**

Question 40

Glycogenesis, enzymes?

Answer 40

Hexokinase, phophoglucomutase, glycogen synthase

Question 41

Glycogenolysis, purpose?

Answer 41

Breaking down glycogen into glucose to provide immediate energy and to maintain blood glucose levels during fasting

Question 42

Glycogenolysis, regulation?

Answer 42

**Stimulated** hormonally by **glucagon** and **epinephrine** **Inhibited** hormonally by **insulin** *Hormonal regulation through cAMP/pKA signalling* **Inhibited** allosterically by **ATP** and and **glucose**

Question 43

Glycogenolysis, enzymes?

Answer 43

**Glycogen** **phosphorylase** catalyzes the sequential phosphorolysis/**breaking down** of **glycogen** (no ATP required) Other enzymes include **ph****osphoglucomutase**and**glu-6-phosphatase**

Question 44

Pentose phosphate pathway, purpose and products?

Answer 44

**2** **phase** alternative process to glycolysis, **glucose oxidation** Produces **2 NADPHs** (reducing power in fatty acid synthesis, eliminating free radicals) and **ribose-5-phosphate** (nucleotide precursor)

Question 45

Pentose phosphate pathway, location?

Answer 45

Cytosol

Question 46

Pentose phosphate pathway, oxidative phase?

Answer 46

**Glucose-6-phosphate** is converted to **ribulose-5-P** with **glucose-6-phosphate dehydrogenase**

Question 47

Pentose phosphate pathway, nonoxidative phase?

Answer 47

**Ribulose-5-phosphate** is converted to **ribose-5-phosphate** and **2 glycolysis intermediates**

Question 48

Fatty acid/beta oxidation, purpose?

Answer 48

**Breaking** **down** fatty acids into **NADH, FADH2, and** **acetyl** **CoA** (for use in Krebs cycle) Huge source of ATP

Question 49

Fatty acid/beta oxidation, location?

Answer 49

**Mitochondria** for eukarytotic cells Cytosol for prokaryotic cells

Question 50

Fatty acid/beta oxidation, process?

Answer 50

**2 carbons** **removed** from fatty acid chain with each round of oxidation, which **produce** single molecules of **acetyl-CoA** Cycle repeats until fatty acid is 2 or 3 carbons long

Question 51

Fatty acid/beta oxidation, enzymes?

Answer 51

For **saturated** fatty acids - **dehydrogenase** For **unsaturated** fatty acids - **isomerase**

Question 52

Fatty acid/beta oxidation, requirements?

Answer 52

**ATP** to activate, **FAD** and **NAD+** for each 2C to produce FADH2 and NADH

Question 53

Fatty acid/beta oxidation, precursor/enzyme for metabolism?

Answer 53

**Before** **oxidation**, fatty acids must be **activated** by addition of **S-CoA** to carboxylic end (in cytoplasm) **Lipase** is an enzyme that breaks down triglycerides

Question 54

Fatty acid ketogenesis, purpose?

Answer 54

Under metabolic conditions associated with _high rate of fatty acid oxidation_ (**starvation**, keto), the **liver** produces ketone bodies from **acetyl-CoA** as a source of energy. These ketone bodies can enter brain or other organisms to be **reconverted** **to acetyl-CoA**

Question 55

Fatty acid ketogenesis, ketone bodies?

Answer 55

**Acetone, Acetoacetate, 3-hydroxybutyrate** (Acetoacetate can split to form the other two)

Question 56

Fatty acid ketogenesis, regulation?

Answer 56

Triggered by **low blood glucose and low glycogen** _OR_ Triggered by **high blood glucose and low insulin**

Question 57

Fatty acid synthesis, purpose and precursor molecules?

Answer 57

Creation of fatty acids from **activated** **acetyl-COA** and **malonyl-CoA**

Question 58

Fatty acid synthesis, location?

Answer 58

Cytosol

Question 59

Fatty acid synthesis, process?

Answer 59

**Acetyl-CoA** and **Malonyl-CoA** are activated by **ACP** (acyl carrier protein) to **acetyl-_ACP_** and **Malonyl-_ACP_** **Acetyl-CoA** is converted to **Acetyl-FAS (**fatty acid attached) **Fatty acid synthase** combines malonyl-ACP with acetyl **2 NADPH's used** (per round) to remove ketone and double bond *Cycle repeats, adding activated **malonyl-CoA** to create fatty acid chain (typically around 16 carbons)*

Question 60

Protein catabolism, 3 endpoints?

Answer 60

Can be used to **construct other proteins** Amino end can be used for **nucleotides** or **urea** Remaining carbon skeleton can be converted to **acetyl-CoA** or **glucose (glycolytic or ketogenic pathways)**

Question 61

Protein catabolism, process?

Answer 61

**Hydrolysis** breaks **peptide** **bond** to detach amino acid from peptide chain **Amino acid deamination** utilizes NAD+ and produces NADH

Question 62

Insulin and Glucagon regulation

Answer 62

- Insulin helps the cells absorb glucose, promotes - Glucagon instructs the liver to release stored glucose, promotes