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Fall 2019HFH1104
Armen ZakarianOffice: Chemistry Bldn 2217
Chem 109 CBioorganic Compounds
http://labs.chem.ucsb.edu/~zakariangroup/courses.html
CLAS Instructor: Dhillon [email protected]
• Chapter 23. Organic Chemistry of Coenzymes.
Sections 23.5 – 23.8 inclusively
• Chapter 24. Organic Chemistry of Metabolic Pathways.
Sections 24.1 – 22.10 inclusively
•
no additional material (like carbohydrate tables in M1) will be necessary
Midterm 3
Wednesday, November 20, HFH 1104, 8 – 8:50 am
summary of previous sections
Coenzymes (chapter 23)
PLP (B6, 5 amino acid reactions, transimination)
B12 (radical mechanism, Co, 1,2-isomerizations, mutases)
THF (folic acid, one-carbon group transfer, synthesis of dTMP)
vitamin KH2 (carboxylation of glutamate side chains, base form, epoxide, dioxetane)
Metabolism (chapter 24) 4 stages of catabolism ATP structure/properties beta-oxidation
glycolysis pyruvate
citric acid cycle reactions, coenzymes, enzymes
PRACTICE PROBLEM What carbon atoms of glucose end up in ethanol under anaerobic conditions in yeast?
Chapter 24
PRACTICE PROBLEM Which acyl group is transferred by thiamine pyrophosphate in the fourth reaction of the citric acid cycle?
PRACTICE PROBLEM Which of the 8 enzymes in the citric acid cycle has a name that refers to the reverse reaction?
Which of the 10 enzymes in glycolysis has a name that refers to the reverse reaction?
Enzymes in CAC:
1. citrate synthase (AcSCoA + oxaloacetate ! citrate)2. aconitase (citrate ! isocitrate)3. isocitrate dehydrogenase (isocitrate ! alpha-ketoglutarate)4. alpha-ketoglutarate dehydrogenase (alpha-ketoglutarate ! succinyl-CoA)5. succinyl-CoA synthase (succinyl-CoA ! succinate)6. succinate dehydrogenase (succinate ! fumarate)7. fumarase (fumarate ! (S)-malate)8. malate dehydrogenase (malate ! oxaloacetate)
Chapter 24
Enzymes in glycolysis:
1. hexokinase (Glu ! G6P)2. phosphoglucose isomerase (G6P ! F6P)3. phosphofructo kinase (F6P ! F1,6BP)4. aldolase (F1,6BP ! GAD3P + DHAP)5. triosephosphate isomerase (DHAP ! GAD3P)6. GAD3P dehydrogenase (GAD3P ! 1,3BPG)7. phosphoglycerate kinase (1,3BPG ! 3PG)8. phosphoglycerate mutase (3PG ! 2PG)9. enolase (2PG ! PEP) 10. pyruvate kinase (PEP ! pyruvate)
Chapter 24
Chapter 25: Lipids [25.1-25.7, 25.10]
o Lipids are naturally occurring organic compounds that are not soluble in water, but soluble in non-polar solvents
Compounds containing fatty acids
o Waxes: (beewax, leaf and feather coatings etc.)
o Animal and plant triglycerides (oils and fats)
o Phospholipids: components of cell membranes
O
O
o Esters of fatty acids and glycerol are triglycerides [components of fats and oils]
Chapter 25: Triglycerides
o Solid triglycerides [fats] have mostly saturated carbon chainso Liquid triglycerides [oils], higher content of unsaturated carbon chains
Chapter 25
Problem 3. Draw a structure of an optically inactive fat that, when hydrolyzed, gives glycerol, one equivalent of lauric acid, and two equivalents of stearic acid.
o Converting oils to fats found in margarine and shortening
Chapter 25
O
O
O
O
OO
“trans fat”
O
O
O
O
OO
oil
O
O
O
O
OO
margarine/shortening
H2Pd/C
o Sodium or potassium salts of fatty acids are soaps
Chapter 25: Soaps
o Sodium or potassium salts of fatty acids are soapso Soaps form micelles in water, which trap non-polar
contaminants
Chapter 25: Soaps
o Detergents are [potassium] salts of benzenesulfonic acids
Chapter 25: Soaps
o Phospholipids: cell membranes and lipid bilayers
Chapter 25: Phospholipids
o Phospholipids: cell membranes and lipid bilayers
Chapter 25: Phospholipids
o Phosphoglycerides: derived from glycerol
Chapter 25: Phospholipids
O
O
O
O
OPRO O
O
R = CH2CH2NH3+
phosphatidylethanolamine
R = CH2CH2NMe3+
phosphatidylcholine
R = CO2
NH3+
phosphatidylserine
o Sphingolipids: cell membranes in the brain
Chapter 25: Phospholipids
NH2HO
OH sphingosine
both stereocenters have S configuration
o Sphingolipids: cell membranes in the brain
Chapter 25: Phospholipids
NH2HO
OH sphingosine
both stereocenters have S configuration
NHHO
O ROP
O
O
O+H3N
NHHO
O ROP
O
O
O+Me3N
with phosphoethanolamine
with phosphocholine
sphingomyelins
Chapter 25: Prostaglandins
CO2H
PG C20 carbon skeleton
OR1
R2
OR1
R2
OR1
R2
PGA PGB PGC
HOR1
R2O
O
HO
CO2H
OH
PGD PGE1
O
HO OH
PGE2
CO2H
enones
beta-hydroxy ketones
o Prostaglandins: found in all body tissues at low levelso regulatory molecules for many functions, including response to injury, inflammation and pain
o Prostaglandins: found in all body tissues at low levelso regulatory molecules for many functions, including response to injury, inflammation and pain
Chapter 25: Prostaglandins
CO2H
PG C20 carbon skeleton
OR1
R2
OR1
R2
OR1
R2
PGA PGB PGC
enones
1,3-diols
HO
HO OH
PGF2α
CO2H
HO
HO OH
PGF2β
CO2H
Chapter 25: Prostaglandins
CO2H
H H
cyclooxygenase(COX)
target of NSAIDs CO2H O O
CO2H
OO
O O
O
CO2H
O
O
OH
hydroperoxidase
OH
CO2H
O
O prostaglandins (thromboxanes, etc.)
Chapter 25: Prostaglandins
CO2H
H H
cyclooxygenase(COX)
target of NSAIDs CO2H O O
CO2H
OO
O O
O
CO2H
O
O
OH
hydroperoxidase
OH
CO2H
O
O prostaglandins (thromboxanes, etc.)
Chapter 25: Prostaglandins
CO2H
H H
cyclooxygenase(COX)
target of NSAIDs CO2H O O
CO2H
OO
O O
O
CO2H
O
O
OH
hydroperoxidase
OH
CO2H
O
O prostaglandins (thromboxanes, etc.)
Chapter 25: Prostaglandins
CO2H
H H
cyclooxygenase(COX)
target of NSAIDs CO2H O O
CO2H
OO
O O
O
CO2H
O
O
OH
hydroperoxidase
OH
CO2H
O
O prostaglandins (thromboxanes, etc.)
Chapter 25: Prostaglandins
CO2H
H H
cyclooxygenase(COX)
target of NSAIDs CO2H O O
CO2H
OO
O O
O
CO2H
O
O
OH
hydroperoxidase
OH
CO2H
O
O prostaglandins (thromboxanes, etc.)
Chapter 25: Terpenes
Terpenes are a highly diverse group of compounds that contain 10, 15, 20, 25, 30, or 40 carbons. More than 20,000 terpenes are found in nature
Chapter 25: Terpenes
Terpenes are made by joining isoprene units, generally in a head-to-tail fashion.
The compound actually used in the biosynthesis is isopentenyl pyrophosphate, not isoprene.
Chapter 25: Terpenes
monoterpenes sesquiterpenes diterpenes triterpenes
10 carbons (two isoprene units) 15 carbons 20 carbons 30 carbons
tetraterpenes 40 carbons (carotenoids)
Chapter 25: Terpenes
let’s identify isoprene units in cholesterol
HOH
H
H
H
