Lecture 2

Question 1

Bioenergentics is affected by 3 factors? What are they and explain about each.

Answer 1

Enthalpy (H) - Total heat content
Entropy (S) - Disorder
Free energy (G) - Energy available to do chemical work and a measure of the spontaneity of chemical reactions

Temperature in Kelvin
K = C + 273

Question 2

What is ΔG° and explain the conditions

Answer 2

Standard free energy at standard conditions
1 Molar
298 Kelvin
1 atm

Question 3

What is the standard free energy of hydrolysis of ATP?

Answer 3

ΔG° is -7.3 kcal/mol for each of the 2 terminal phosphate groups

Question 4

Locations of metabolic processes/pathways

Answer 4

Glycolysis - Cytosol of cell
Kreb cycle - matrix of mitochondria
ETC - Inner membrane of mitochondria

Question 5

Process of ETC along with complexes

Answer 5

NADH donates electrons to Complex I which then transfers the hydrogen atoms to Coenzyme Q (Ubiquinone). Succinate dehydrogenase in Kreb cycle reduces succinate to form FADH2 which then transfers electrons to CoQ. CoQ is a mobile carrier than then accepts hydrogen atoms from complex I and II to transfer to complex III. Electrons pass from complex III to complex IV which then reduces O2 to water. The protons in the intermembrane space then get pumped out by ATP synthase (Complex V) to make ATP.

Question 6

What does incomplete reduction of oxygen to water produce?

Answer 6

Reactive oxygen species such as superoxide and hydroxyl radical. These can be cleaned up with enzymes such as superoxide dismutase, catalase, and glutathione peroxidase.

Question 7

What is the direction of electron flow in terms of standard reduction potential

Answer 7

From more negative E to higher/positive E.
More negative the E means more likely to give up electrons.

Question 8

How much ATP does NADH and FADH2 generate?

Answer 8

NADH - 2.5 ATP 4 from I, 4 from III, 2 from IV = 10 H+ /4 = 2.5
FADH2 - 1.5 ATP 4 from III, 2 from IV = 6 H+ /4 = 1.5
4 H+ going through complex V produces 1 ATP

Question 9

What do uncoupling proteins (UCPs) do to the ETC and what is produced as a result?

Answer 9

Uncoupling proteins increase the permeability of the inner mitochondrial membrane and these carrier proteins allow protons to re-enter the mitochondrial matrix to produce heat (Known as nonshivering thermogenesis)

Question 10

Names of carbohydrates based on number of carbons
Also classification of carbohydrates.

Answer 10

3 Carbons: Trioses
4 Carbons: Tetroses
5 Carbons: Pentose
6 Carbons: Hexoses
7 Carbons: Heptoses
9 Carbons: Nonoses

Oligosaccharides - 3-10 monosaccharides
Polysaccharides - 10 monosaccharides

Question 11

What are aldoses and ketoses?

Answer 11

Aldoses - Carbohydrates with aldehyde as their most oxidized functional group
Ketoses - Carbohydrates with keto as their most oxidized group

Question 12

What are isomers, epimers, and enantiomers?

Answer 12

Isomers - Compounds that have the same chemical formula but different structures
Epimers - Carbohydrate isomers that differ in configuration around only 1 specific carbon atom
Enantiomers - Isomers that are mirror images of each other

Most sugars are D-sugars
Racemases are enzymes that can interconvert D and L isomers

Question 13

What is the difference between pyranose and furanose?

Answer 13

Pyranose is a 6 membered ring while furanose is a 5 membered ring

Alpha is on the right and Beta is on the left in fisher projection
Alpha is on the bottom and Beta is on the top in haworth projection

Question 14

Aldehyde group is a what agent and all monosaccharides are what sugar?

Answer 14

Aldehyde groups are reducing agents and all monosaccharides are reducing sugars

Question 15

What is the importance of benedict’s reagent or Fehling’s soluition?

Answer 15

They can react with sugar to become reduced and colored and making the aldehyde group oxidized into a carboxyl group.

Question 16

What do glycosyltransferases do?

Answer 16

They link sugars to form glycosidic bonds

Question 17

Where does digestion of carbohydrates stop and why along with what enzyme is affected?

Answer 17

Digestion of carbs stops in the stomach due to the acidic environment in the stomach. This high acidity inactivates salivary a-amylase (key enzyme doing digestion). The contents reach the small intestine where the pancreas secretes bicarbonate to neutralize the acid and pancreatic a-amylase can continue starch digestion

Question 18

What do glycosidases do?

Answer 18

Glycoside hydrolases hydrolyze glycosidic bonds to create monosaccharides (glucose, galactose, fructose)

Question 19

What is the difference between amylose and amylopectin? What is the function of amylase?

Answer 19

Amylose is a straight chain of starch while amylopectin is a branch chain of starch. Amylase hydrolyzes random a(1->4) bonds

Question 20

Where are GLUT-2 and GLUT-4 abundant and why is GLUT-4 insulin-dependent?

Answer 20

GLUT-2 is abundant in pancreatic B-cells, liver and kidney
GLUT-4 is abundant in adipose tissue and skeletal muscle and is insulin-dependent since GLUT-4 is found in the cytosol but moves into the membrane to work through insulin.

Question 21

How does glucose, galactose, and fructose enter into enterocytes (Cell of the intestinal lining)?

Answer 21

Glucose and galactose enter through Sodium dependent-glucose transporter (SGLT) while fructose enters through GLUT-5 in which they move through secondary active transport. The sodium-potassium pump causes the concentration gradient of Na to be higher on the outside which allows sodium to go down its concentration gradient into the cell and the monosaccharides are coupled along. All 3 then can enter the blood vessel through GLUT-2 transporter. This occurs in the epithelial cells of the intestine.

Question 22

Why do any defects in a specific disaccharidase activity cause diarrhea

Answer 22

Defects cause the passage of undigested carbohydrates into the large intestine which then causes water to be drawn from the mucosa into the large intestine causing diarrhea, bacterial fermentation of the remaining carbohydrate plus large volumes of CO2 and H2 gas causing abdominal cramps and flatulence.

Question 23

Why is the pentose phosphate pathway important?

Answer 23

It produces NADPH (Reducing agent in fatty acid synthesis) and Ribose (Required for nucleic acid biosynthesis)
This pathway occurs in cytosol

Question 24

What is the importance of phosphorylating glucose?

Answer 24

Phosphorylation of glucose traps it into the cell through enzyme hexokinase/glucokinase

Question 25

Where are glucokinase and hexokinase found?

Answer 25

Hexokinase I-III isozymes in most tissues. Glucokinase is a form of Hexokinase IV that is found in the liver and pancreas since a large amount of glucose is in the liver and pancreas Glucokinase has a higher Vmax and higher Km than than hexokinase I-III

Question 26

Major regulatory points in glycolysis

Answer 26

1. Glucose -> G-6-P through hexokinase/glucokinase in which hexokinase is inhibited by G-6-P and glucokinase inhibited by F-6-P to prevent backward flow. 2. Irreversible phosphorylation of F-6-P to fructose-1,6-bisphosphate is catalyzed by phosphofructokinase-1 (PFK-1) and this is the most important control point/rate limiting/committed step of glycolysis 3. PEP is converted to pyruvate by pyruvate kinase and is an irreversible reaction of glycolysis

Question 27

What does aldolase do in glycolysis?

Answer 27

Aldolase converts the 6 carbon Fructose-1,6-bisphosphate into 3 carbon molecules (G-3-P and Dihydroxyacetone phosphate). Only G-3-P continues onto glycolysis

Question 28

What is the function of enolase and what can it be inhibited by?

Answer 28

Dehydrates 2-phosphoglycerate to phosphoenolpyruvate (PEP) Inhibited by fluoride

Question 29

What does glycolysis yield?

Answer 29

Glucose + 2 Pi + 2 ADP + 2 NAD+ = 2 pyruvate + 2 NADH + 2 ATP

Question 30

How does pyruvate convert to Acetyl-CoA?

Answer 30

Pyruvate dehydrogenase

Question 31

What are the 3 enzymes of PDH complex along with the coenzyme each needs?

Answer 31

1. Pyruvate dehydrogenase (E1) - Requires Thiamine pyrophosphate (TPP) 2. Dihydrolipoyl transacetylase (E2) - Requires lipoic acid and CoA which is why arsenic poisoning occurs due to inhibition of E2 since it requires lipoic acid as a coenzyme 3. Dihydrolipoyl dehydrogenase (E3) - FAD and NAD+

Question 32

Steps in TCA cycle where NADH and FADH2 are produced

Answer 32

NADH: 1. Isocitrate -> a-ketoglutarate through Isocitrate dehydrogenase 2. a-ketoglutarate -> Succinyl-CoA through a-ketoglutarate dehydrogenase 3. Malate -> Oxaloacetate through malate dehydrogenase FADH2: 1. Succinate -> Fumarate through succinate dehydrogenase (Complex II)

Question 33

What enzyme isomerizes citrate to isocitrate?

Answer 33

Aconitase

Question 34

What does isocitrate dehydrogenase do/produce and why is it important?

Answer 34

Isocitrate dehydrogenase catalyses the irreversible oxidative decarboxylation of isocitrate to form a-ketoglutarate in which 1 NADH, 1 CO2 is produced and this is one of the rate-limiting steps of the TCA cycle.

Question 35

Where does GDP get phosphorylated to GTP in the TCA cycle?

Answer 35

When succinyl CoA is cleaved to form succinate by the enzyme succinate thiokinase (succinyl CoA synthetase)

Question 36

3 Enzymes that regulate the TCA cycle

Answer 36

1. Citrate synthase 2. Isocitrate dehydrogenase 3. a-ketoglutarate dehydrogenase complex

Question 37

Important Steps in Gluconeogenesis

Answer 37

1. Pyruvate to Oxaloacetate by pyruvate carboxylase 2. oxaloacetate to Phosphoenolpyruvate by phosphoenolpyruvate carboxykinase 3. Fructose-1,6-Bisphosphate to fructose-6-phosphate through fructose-1,6-bisphosphatase 4. Glucose-6-phosphate to glucose through glucose-6-phosphatase

Question 38

Why does phosphorylation of glycerol to glycerol-3-phosphate occur in the liver?

Answer 38

Liver contains glycerol kinase enzyme whereas adipocytes lack glycerol kinase

Question 39

Amino acids that form pyruvate and oxaloacetate

Answer 39

Pyruvate: 1. Alanine 2. Serine 3. Glycine 4. Cysteine 5. Threonine Oxaloacetate: 1. Aspartate 2. Asparagine

Question 40

Location of enzymes responsible for synthesis of PEP from pyruvate

Answer 40

Pyruvate carboxylase is located in the mitochondria to convert pyruvate to oxaloacetate PEP carboxykinase is located within the cytoplasm and converts oxaloacetate to PEP

Question 41

Where is Glucose-6-phosphatase found?

Answer 41

Found only in liver and kidney to catalyze the irreversible hydrolysis of G-6-P to form glucose and Pi

Question 42

When is insulin released vs glucagon?

Answer 42

Insulin is released in a fed/full state to take in glucose through the bloodstream and even store some as glycogen. Glucagon is released in a hungry state to signal liver and muscle cells to convert glycogen into glucose for energy. Epinephrine similar to glucagon in which it stimulates glycogenelysis and inhibits glycogenesis

Question 43

Why does the muscle not convert G-6-P into glucose like the liver does?

Answer 43

Muscle does not have glucose-6-phosphatase to convert G6P into glucose so G6P enters into glycolysis immediately

Question 44

What is glycogen composed of and what bonds. Also where does glycogen synthesis occur?

Answer 44

Glycogen is synthesized from molecules of a-D-glucose with the primary glycosidic bond being a(1->4) linkage and branching containing a(1->6) linkage occurring after 8-10 glucosyl residues. Glycogen is synthesized in the cytosol and requires energy from UTP.

Question 45

What does glycogen synthase require for synthesis?

Answer 45

A primer either through a fragment of glycogen or through a protein called glycogenin

Question 46

What enzyme is responsible for degradation of glycogen?

Answer 46

Glycogen phosphorylase cleaves the a(1->4) glycosidic bonds to produce glucose-1-phosphate

Question 47

Which enzyme removes the single remaining glucose reside attached in the a(1->6) linkage to release free glucose?

Answer 47

Amylo-a(1->6)-glucosidase

Question 48

What enzyme is responsible for the conversion of G-1-P to G-6-P and where is it located?

Answer 48

Phosphoglucomutase and located in the cytosol

Question 49

What is the ratio of glucose-1-p to glucose in glycogen degradation?

Answer 49

8 G-1-P : 1 Glucose

Question 50

Activated form of glycogen phosphorylase vs glycogen synthase

Answer 50

Activated form of glycogen phosphorylase is the phosphorylated form whereas activated form of glycogen synthase is the dephosphorylated form

Question 51

3 Disaccharides and what they are composed of

Answer 51

Sucrose - Glucose + Fructose Lactose - Galactose + Glucose Maltose - Glucose + Glucose

Question 52

What does Glucose-6-phosphate dehydrogenase do?

Answer 52

Enzyme responsible for turning Glucose-6-phosphate into 6-Phosphogluconolactone in the pentose phosphate pathway

Question 53

What are the functions of NADPH?

Answer 53

1. Used in reductive biosynthesis (Fatty acids) 2. Reduction of H2O2 (Forms reduced glutathione) 3. Maintain hemoglobin in its reduced form and protects against hemolysis

Question 54

What are glycosaminoglycans composed of?

Answer 54

They are based on a repeating disaccharide unit and contain amino sugars and acidic sugars (Hence negatively charged)

Question 55

What is mucopolysaccharidosis?

Answer 55

Hereditary disorder in which GAG accumulate in tissues causing symptoms such as skeletal and extracellular matrix deformities and intellectual disability (Mainly affects brain) -Results in deficiency of lysosomal hydrolases

Question 56

What are proteoglycans composed of?

Answer 56

They are constructed of protein and glycosaminoglycans. (Protein backbone with disaccharide branch chains)

Question 57

What are glycoproteins and how are they different from proteoglycans?

Answer 57

Glycoproteins are proteins to which oligosaccharides are covalently attached. They differ in that the length of the carbohydrate chain in glycoproteins is relatively short (2-10 sugar residues) whereas glycosaminoglycans of proteoglycans are much longer. Deficiency of lysosomal hydrolases results in oligosaccharidosis which results in partially degraded structures in the lysosome.