Biochem Exam II

Question 1

How is the Heme prosthetic group stabilized in myoglobin?

Answer 1

• A Fe(II) molecule is stabilized within a heterocyclic ring structure of 4 pyrrole groups connected by methene bridges
• The Fe(II) molecule is coordinated by the 4 porphyrin N atoms and an N atom of His F8, the proximal histidine
• O2 binds to Fe(II) at the 6th ligand position and His E7, the distal histidine, binds to the O2
• 2 hydrophobic side chains ValE11 (left) and Phe CD1 (right) give additional structural stability

Question 2

What happens to the myoglobin molecule when meat spoils?

Answer 2

The helices that stabilize the heme structure begin to degrade which allows the hydrophobic binding pocket to get disrupted. This means the ferris (Fe(II)) ion is able to be oxidized into a ferric (Fe(III)) ion meaning O2 reacts with Fe(II) and does not bind to the pocket containing iron, which causes the meat to turn grayish in color. Heat (cooking the meat) speeds up this process. When the heme is disrupted, Fe(II) gets oxidized meaning oxygen does not bind to the hydrophobic binding pocket and myoglobin cannot function.

Question 3

What is the function of myoglobin?

Answer 3

Myoglobin facilitates O2 diffusion in muscle. This is slow due to low O2 solubility. Myoglobin also has the effect of storing O2 within muscles.

Question 4

How do the subunits of hemoglobin interact?

Answer 4

-a1-B1 and a2-B2 interface at 35 residue contacts
- a1-B2 and a2-B1 interface at 19 residue contacts

Question 5

What are the structural differences between oxyhemoglobin (R state) and deoxyhemoglobin (T state)?

Answer 5

In the presence of oxygen one aB dimer is rotated ~15 deg closer to the other aB dimer along a 360 deg axis

Question 6

What happens when hemoglobin is oxygenated?

Answer 6

When oxygen binds to hemoglobin, the Fe(II) atom is pulled 0.4 angstroms into the heme plane shifting the alpha helix F, which has the effect of shifting the helix into a tighter conformation. When this occurs an R state is formed from the deoxygenated T state.

Question 7

What do the oxygen binding curves for myoglobin and hemoglobin suggest about their functions?

Answer 7

In the lungs the O2 partial pressure is 100 torr and in the tissues the O2 partial pressure is 20 torr. As myoglobin moves from the lungs to the tissues, even as the O2 partial pressure greatly decreases, the fractional saturation of myoglobin only decreases by around 7%, making it a poor oxygen depositor. This suggests that myoglobin functions to retain O2 intracellularly for storage rather than deposit it to tissues.

In contrast, as hemoglobin moves from the lungs to the tissues, where there is a lower O2 partial pressure, the fractional saturation of hemoglobin decreases by 66%, meaning hemoglobin is much more likely to give up its oxygen as it goes from a high to a low partial pressure of oxygen than myoglobin. This suggests that hemoglobin functions as an oxygen depositor to tissues.

Question 8

How can the p50 illustrate that hemoglobin is able to more readily deliver oxygen to tissues than myoglobin?

Answer 8

The p50 refers to the partial pressure of O2 that is required to give 50% oxygen binding saturation. The p50 for myoglobin is 2.8 torr and the p50 for hemoglobin is 26 torr. Since we know the partial pressure of oxygen at tissues is 20 torr, the p50 can give an estimate of the saturation for myoglobin and hemoglobin at tissues. We know hemoglobin has an oxygen saturation of lower than 50% and myoglobin has an oxygen saturation of much higher than 50% at tissues, and a lower oxygen binding saturation for Hb suggests Hb is better able to readily deliver O2 than Mb.

Question 9

How does the decrease of blood pH at tissue capillaries allow for the release of more O2 from hemoglobin (The Bohr Effect)?

Answer 9

When the blood pH decreases, this means excess protons are present at tissue capillaries. This results in increased oxygen deposition since when gas exchange occurs, Hemoglobin takes up the excess H+, and the H+ forms more ionic interactions that stabilize the deoxygenated T state rather than the oxygenated R state, which results in more O2 being released.

This means that the fractional saturation of O2 is decreased when pO2 is 20 torr at tissue capillaries, and this has the effect of shifting the binding curve to the right. A 0.2 decrease in blood pH generally results in a ~10% increase of the difference in fractional saturation between the lungs and tissues, resulting in ~10% more oxygen deposition.

Question 10

What are three different ways the Bohr effect is used to promote oxygen release in hemoglobin?

Answer 10

• a red blood cell enzyme carbonic anhydrase catalyzes the production of bicarbonate and protons and decreases blood pH at tissue capillaries
  H2O + CO2 –> H+ + HCO3-
• the formation of lactic acid also decreases blood pH at tissue capillaries, generally in active muscles (~10% more O2 deposition)
• carbamate is formed as CO2 combines with the N-terminal of amino acids and this reaction produces protons which increase blood pH

Question 11

How can D-2,3-biphosphoglycerate control oxygen binding/deposition?

Answer 11

D-2,3-biphosphoglycerate is a highly negatively charged molecule that binds to a positively charged, allosteric site within hemoglobin and stabilizes the T state.

The presence of BPG shifts the O2 fractional saturation curve to the right (higher pO2) releasing more O2. The absence of BPG shifts the curve to the left releasing less O2.

Question 12

Why does O2 flow from maternal oxyhemoglobin to fetal deoxyhemoglobin?

Answer 12

BPG binds tighter to adult hemoglobin than fetal hemoglobin meaning adult Hb has a lower affinity for O2 and fetal Hb has a higher affinity. Since BPG concentration is the same in fetal and maternal circulation, this results in O2 moving from maternal red blood cells to fetal red blood cells. Fractional saturation is higher in fetal red blood cells at the same pO2 than maternal red blood cells enabling this flow.

Question 13

What digestive enzymes are present in the mouth and what are their functions?

Answer 13

Salivary a-amylase hydrolyzes a 1-4 bonds that form polysaccharide chains in sugars but not a 1-6 bonds that link branching chains together. This results in broken down sugars being formed.

Lingual lipase begins to hydrolyze triglycerides (triacylglycerol) into diacylglycerol and monoacylglycerol.

Question 14

What digestive enzymes are generally found in the stomach and how do they function?

Answer 14

Pepsin hydrolyzes proteins after an acidic pH of 1-2 in the stomach denatures the food.

Question 15

What digestive molecules are commonly found in the small intestine?

Answer 15

Oligopeptides and acidic digestive production from the stomach stimulate the production of secretin and cholecystokinin (CCK) from the small intestine respectively.

Secretin stimulates sodium bicarbonate (NaHCO3) secretion from the pancreas to neutralize the acidic contents of the stomach

After the contents are neutralized, CCK stimulates the pancreas to release numerous enzymes and stimulates the gallbladder to release bile salts, which aid in fatty acid digestion.

Question 16

How are zymogens different from enzymes?

Answer 16

Digestive enzymes tend to be secreted as zymogens (also known as inactive precursors or proenzymes) that then get activated into enzymes

Question 17

How is pepsinogen activated into pepsin?

Answer 17

Pepsinogen has a low level of enzyme activity that allows it to activate itself to some capacity in an acidic environment such as the stomach. The active pepsin enzymes can then activate the remaining pepsinogen zymogens.

Question 18

How is trypsinogen activated into trypsin? What is the function of trypsin?

Answer 18

Enteropeptidase is secreted by epithelial cells as a functional enzyme and activates trypsinogen into trypsin. Trypsin can then further activate the remaining pancreating zymogens such as elastase, carboxy-peptidase, chymotrypsin, lipase, and can further activate trypsinogen into trypsin.

Question 19

What are the functions of the pancreatic enzymes?

Answer 19

Lipase - further breaks down fatty acid chains, removes them one at a time from the triglyceride

Chymotrypsin - cleaves the peptide bonds of aromatic amino acids

Trypsin - cleaves the peptide bonds of basic amino acids

Carboxypeptidase - removes amino acids one at a time from the C terminus of an amino acid chain

Elastase - general protease that breaks down proteins

Question 20

What role does peptidase play in the breakdown of amino acids?

Answer 20

Peptidases complete the breakdown of oligopeptides into singular amino acids, tripeptides, and dipeptides until only amino acids are present that can be transported through the bloodstream

Question 21

What enzymes digest sugars in the small intestine?

Answer 21

Pancreatic a-amylase hydrolyzes a-1-4 bonds in polysaccharides to produce maltotriose, maltose, and a-limit dextrin

These enzymes are sugar enzymes that are located on the epithelial cell surface

Maltase - converts maltose into glucose
a-glucosidase - digests maltotriose and other oligosaccharides
a-dextrinase - digests the limit-dextrin
sucrase - digests sucrose to glucose and fructose
lactase - digests lactose to glucose and galactose

Question 22

What are different ways food intake is regulated?

Answer 22

CCK and glucagon-like peptide 1 is secreted from the small intestine, acts through a specific G-protein linked receptor in the brain, and induces feelings of satiety that inhibit further eating

Leptin is secreted from adipocytes, acts through specific receptors in the brain, and also induces feelings of satiety that inhibit further eating

Insulin is secreted from B-cells in the pancreas in response to elevated blood glucose levels and acts through tyrosine kinase receptors primarily in muscle cells and adipocytes in order to induce glucose uptake for storage

Question 23

What is the difference between constitutional isomers and steroisomers?

Answer 23

Isomers have the same molecular formula but a different structure. Constitutional isomers have the same chemical composition but differs in the order of attachments (glyceraldehyde and dihydroxyacetone). Stereoisomers are connected in the same order but differ in spatial arrangement

Question 24

What are the two types of steroisomers?

Answer 24

Enantiomers - made up of nonsuperimposable mirror images (D and L glyceraldehyde)

Diasteroisomers - made of of molecules that are nonsuperimposable and not mirror images

Question 25

What are the different types of diasteroisomers?

Answer 25

Epimers differ at one asymmetric carbon atom

Anomers are a type of epimer where two molecules differ at an acetyl carbon, which is a carbon bound to two O atoms

Question 26

How do dihydroxyacetone and glyceraldehyde differ?

Answer 26

They are constitutional isomers since they have the same composition but dihydroxyacetone is a ketone and glyceraldehyde is an aldehyde

Question 27

How do D-Glucose and D-Galactose differ?

Answer 27

They are epimers that differ in conformation at the C4 carbon

Question 28

What are different sugar phosphates and their functions?

Answer 28

Sugar phosphates have substituted phosphate groups O-Pi instead of O-H groups. Glucose-6-phosphate is the first intermediate in the digestion of glucose, Dihydroxyacetone phosphate (DHAP) plays a major biochemical role in glycolysis, and Ribose/deoxyribose phosphate forms the backbone of DNA and RNA, where a phosphate group connects the 5’ and 3’ carbons of sugars.

Question 29

What are different types of amino sugars and their functions?

Answer 29

Amino sugars are sugars that contain an amine group in place of a hydroxyl group. Galactoseamine contains an NH2 group at the 2C carbon and serves as a constituent of glycoprotein hormones such as follicle stimulating and luteinizing hormones.

Glucosamine also contains an amine group at the 2C carbon and is a precursor in the biochemical synthesis of glycosylated proteins and lipids.

N-Acetylglucoseamine contains an N-acetyl group in place of a hydroxyl group at the 2C carbon and is found in biopolymers such as bacterial cell walls and chitin.

Question 30

What are acid sugars and their functions?

Answer 30

Acid sugars have an added carboxylic acid group or substituted carboxylic acid group, and they are commonly found in proteoglycans and the intercellular matrix. Galacturonic acid has a COO- group attached to the 5C carbon rather than the CH2OH group found in galactose.

Question 31

Glycogen

Answer 31

Large polymer of glucose in animals, rest are usually found in plants. Contains a-1,4 linkages and a-1,6 branches ever ~10 glucose units

Question 32

Amylose

Answer 32

Type of starch, made up of an unbranched glucose polymer containing a-1,4 linkages

Question 33

Amylopectin

Answer 33

Type of starch, made up of a large polymer of glucose containing a-1,4 linkages and a-1,6 branches every ~30 glucose units

Question 34

Cellulose

Answer 34

Consists of long chains of glucose made up of B-1,4 linkages. Individual chains are connected together via H bonds to produce a strong, insoluble compound.

Question 35

Glycoproteins

Answer 35

Molecules containing protein and carbohydrate components where protein is the largest component by weight. Tends to be found on cell membranes and used for cell recognition and adhesion. Glycosylation is either N-linked (sugar is attached to amide nitrogen in asparagine side chain) or O-linked (sugar is attached to hydroxyl in serine/threonine side chain)

Question 36

Erythropoietin (EPO)

Answer 36

Glycoprotein that stimulates red blood cell production. Consists of 40% carbohydrate (sugar) with 3 N-linked and 1 O-linked amino acids. The addition of amino acids through glycosylation enhances the stability and activity of EPO.

Question 37

Mucins (mucus)

Answer 37

Glycoprotein that provide a barrier that protects epithelial cells from stress induced damage, also used as a lubricant and for hydration. They are predominately carbohydrate and the protein component has a region with numerous Ser and Thr where there is a variable number of tandem repeats and carbohydrates are O-linked.

Question 38

Proteoglycan

Answer 38

Molecule with proteins and carbohydrates where carbohydrates make up a much higher percentage by weight compared to glycoproteins.

Question 39

Aggrecan

Answer 39

Proteoglycan containing 2397 amino acids and a chondroitin sufate and keratan sulfate. Many aggrecans are linked together by hyaluronan (hyaluronic acid). This forms a gel structure which is key for the formation of cartilage.

Question 40

ABO blood groups

Answer 40

Specific carbohydrates on the surface of red blood cells which determine a blood group. All have an O-antigen but A-antigen has an extra Gal-NAcetyl (a-1,3 linkage) and B antigen has an extra Gal (a-1,3 linkage). Glycotransferase enzymes assemble each antigen which is why each antigen looks different and the blood group of offspring is determined by which glycotransferases were inherited.

Question 41

What is the role of hemagglutinin and neuraminidase in viral binding to cells?

Answer 41

Glycan binding proteins facilitate cell-to-cell contact. Hemagglutinin is a viral glycan binding protein that binds to cell receptors containing sialic acid, an acid sugar. Hemagglutinin is located at the ends of oligosaccharide chains on cell surface glycoproteins and glycolipids.

Neuraminidase is a viral enzyme that cleaves the linkage connecting the hemagglutinin from the virus and sialic acid receptor from the host cell and releases the virus. Anti flu pharmaceuticals are designed to inhibit neuraminidase and prevent viruses from becoming released from the surface of host cells to infect other cells. Neuraminidase targets the site where the sialic acid receptors are bounded to the glycan binding proteins and nueraminidase inhibitors bind to the same site so inhibitors are competitive.

Question 42

What occurs during the first stage of glycolysis?

Answer 42

Hexokinase adds a phosphate group from ATP to glucose as it enters the cell and it is converted to Glucose-6-phosphate

Phosphoglucose isomerase isomerizes glucose-6-phosphate is into fructose-6-phosphate. This is an aldose to ketose conversion

Phosphofructokinase phosphorylates fructose-6-phosphate into fructose-1,6-bisphosphate. It adds a phosphate group from ATP and it is an irreversible reaction

Question 43

What occurs during the second stage of glycolysis?

Answer 43

Aldolase splits fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP)

Triose phosphate isomerase isomerizes DHAP into GAP which then continues through glycolysis. This is a ketose to aldose isomerization. The GAP that is produced can already continue down glycolysis

Question 44

How is glyceraldehyde-3-phosphate converted to 1,3-bisphosphoglycerate theoretically? Is that the process that actually occurs in the cell?

Answer 44

Theoretically, Glyceraldehyde-3-phosphate is oxidized into 3-Phospho-glycerate using NAD+ and a dehydration reaction then adds a phosphate group to 3-phosphoglycerate to form 1,3-bisphospoglycerate, an acyl phosphate. However, 3-phosphoglycerate generally isn’t formed as an intermediate in this process since it is stable and a large amount of energy would be required to phosphorylate it with inorganic phosphate. Instead, glyceraldehyde-3-phosphate is oxidized into a thioester intermediate which is less stable, meaning less energy is required to add an inorganic phosphate group and form 1,3-bisphosphoglycerate. Glyceraldehyde-3-phosphate dehydrogenase catalyzes this process and allows for the formation of a thioester intermediate enzyme substrate complex.

Question 45

How does the formation of 3-phosphoglycerate occur in glycolysis? What are the byproducts?

Answer 45

Phosphoglycerate kinase catalyzes the transfer of a phosphoryl group from the acyl-phosphate of 1,3-bisphosphateglycerate to ADP to produce 3-phosphoglycerate and ATP. This is known as substrate level phosphorylation.

Question 46

How is 3-phosphoglycerate converted to 2-phosphoglycerate?

Answer 46

Phosphoglycerate mutase is a phosphorylated enzyme that has a phosphohistidine in the active site that donates its phosphate group to the carbon 2 forming an intermediate 2,3-bisphosphoglycerate. The C3 phosphate is then removed and this leads to the release of 2-phosphoglycerate and reformation of phosphohistidine.

Question 47

What role does the intermediates of the reaction where 3-phosphoglycerate is converted to 2-phosphoglycerate play?

Answer 47

2,3-bisphosphoglycerate is formed as an intermediate, and this is a negatively charged molecule that binds to a positively charged allosteric site of hemoglobin. This binding stabilizes the deoxygenated T state which allows more O2 to be released from hemoglobin.

Releasing more O2 during glycolysis is favorable since when O2 is present, further ATP production can occur from oxidative phosphorylation since pyruvate can be converted to acetyl-CoA, used in the citric acid cycle, and more reducing agents can be produced to donate electrons in the electron transport chain producing more ATP. The electron transport chain also allows more NAD+ to be regenerated for glycolysis.

Question 48

How is 2-phosphoglycerate converted into pyruvate? What is the fate of pyruvate when O2 is not present?

Answer 48

Enolase catalyzes a dehydration reaction where 2-phosphoglycerate becomes phosphoenolpyruvate, which is a molecule with a high phosphoryl-transfer potential.

Pyruvate kinase then catalyzes the reaction where pyruvate and ATP is produced from Phosphenolpyruvate.

When O2 is not present pyruvate is fermented into ethanol or lactate. These processes allow NAD+ to be regenerated and glycolysis to continue

Question 49

What are the steps of ethanol fermentation?

Answer 49

Pyruvate decarboxylase catalyzes the conversion of pyruvate to acetaldehyde by removing the CO2 group from pyruvate

Alcohol dehydrogenase catalyzes the conversion of acetaldehyde to ethanol and NAD+ is regenerated from NADH

Question 50

How does lactic acid fermentation occur?

Answer 50

Lactate dehydrogenase catalyzes the conversion of pyruvate to lactate and NAD+ is regenerated from NADH

Question 51

What are the steps of fructose metabolism?

Answer 51

• Fructokinase converts fructose into fructose-1-phosphate
• Fructose-1-phosphate aldolase cleaves Fructose-1-phosphate is cleaved into glyceraldehyde and DHAP
• Triose phosphate isomerase converts DHAP into glyceraldehyde-3-phosphate which enters glycolytic pathway
• Triose kinase phosphorylates Glyceraldehyde into Glyceraldehyde-3-phosphate which enters glycolytic pathway

Question 52

How is DHAP formed in gluconeogenesis and why is it significant? What molecules are formed as byproducts?

Answer 52

• Glycerol kinase adds a phosphate group from ATP to glycerol to make glycerol-3-phosphate
• Glycerol-3-phosphate dehydrogenase makes DHAP from glycerol phosphate and NADH is formed from NAD+
• DHAP is an intermediate of glycolysis so it can be used in gluconeogenesis to form glucose (glycolysis can be run backwards from here)

Question 53

How is phosphoenolpyruvate formed during gluconeogenesis and why is it significant? What molecules are used and formed as byproducts?

Answer 53

• Lactate dehydrogenase converts lactate into pyruvate and NADH is formed
• Pyruvate carboxylase carboxylates pyruvate into oxaloacetate and CO2, H2O, and ATP is used
• Phosphoenolpyruvate carboxykinase uses a GTP to convert oxaloacetate into phosphoenolpyruvate and CO2 is formed from the carboxyl group in oxaloacetate
• Phosphoenolpyruvate is then converted into glucose for storage

Question 54

The conversion of phosphoenolpyruvate to pyruvate via pyruvate kinase is an irreversible reaction, but how do cells “get around” this irreversible step during gluconeogenesis?

Answer 54

ATP and GTP is used in this reaction to reduce the activation energy required. Pyruvate carboxylase is in the mitochondrial matrix, and phosphoenolpyruvate carboxylase is in the cytoplasm, so oxaloacetate which is synthesized in the mitochondrial matrix must be transported out into the cytoplasm.

Malate dehydrogenase reduces oxaloacetate initially using NADH and malate is then transported across the inner mitochondrial membrane via the malate decarboxylate carrier and malate is then oxidized back into into oxaloacetate via the malate dehydrogenase