Chapters 6, 7, 8, 9, 10, 11, 12 - Enzymes, Carbohydrates, Metabolism, Aerobic Met., Lipids & Membranes, Lipid Metabolism

Characteristics of enzymes

- Increase reaction rates
- Obey the laws of thermodynamics (no effect on Keq)
- Catalyze the forward and backward reactions of reversible rxns
- Usually present in low concentrations because they are not consumed
- Transition state of reacting substrates bound in enzyme active sites

Characteristics shared between chemical catalysts and enzymes

Both catalyze chemical reactions without altering themselves, they accelerate the rate of rxn but do not alter the equilibrium

Enzymes: Carry out specific reactions at moderate temperature, much larger, require unique "active site"

Chemical catalysts: Accelerate wide variety of chemical reactions and most of them need additional input of energy

Emil Fischer

"Lock and Key"

Koshland

Variation of lock and key but with "induced fit" to take into account conformational flexibility

Category 1 of Enzyme: Oxidoreductases

Catalyze redox reactions

Category 2 of Enzyme: Transferases

Catalyze the transfer of groups from one molecule to another. Common prefix "trans-"

Category 3 of Enzyme: Hydrolases

Catalyze breakage of chemical bonds with the addition of water. Ex: peptidases

Category 4 of Enzyme: Lyases

Catalyze reactions in which groups are removed to form a DOUBLE BOND or are added to one

Category 5 of Enzyme: Isomerases

Intramolecular rearrangements

Category 6 of Enzyme: Ligases

Catalyze bond formation between two substrate molecules. Energy supplied by ATP hydrolysis. Common term "synthetase"

Turnover number

Quantity of substrate in moles converted to product per second by one mole of enzyme

Enzyme activity

Measured in international units. One IU is the amount of enzyme that produces 1 micromole of product per minute

Specific activity

IU per milligram of protein. 'katal'

Katal

transformation of 1 mole substrate to product per second

Slope =

Km/Vmax

Irreversible inhibition

Inhibitor binds covalently to enzyme and inactivates it. ex: Mercury and silver bind to the sulphahydryl group of protein

Reversible inhibition

Inhibitor is bound through noncovalent bonds, can dissociate. Competitive and noncompetitiveC

Competitive inhibition (reversible)

Competitive inhibitor closely resembles the true substrate, it binds to active site and forms enzyme-inhibitor complex. This interferes with product formation and results in a decline in enzymatic activity

Noncompetitive inhibition (reversible)

Inhibitor binds at an allosteric site, does not interfere with binding of enzyme to active site. Brings about conformational changes.

Enzyme catalysis factors:

1. Proximity and strain
2. Electrostatic effect - dipoles of active site and substrate
3. Acid base catalysis - side chain interference, protons
4. Covalent catalysis - Unstable covalent bond that forms between enzyme and substrate which forms product

Cofactors

1. Metal ions: Transition metals and alkaline metals. Transition most often involved in catalysis due to their electronic structure
2. Coenzyme: Derived from vitamins

Enzyme regulation:

1. genetic control
2. covalent modification
3. allosteric regulation
4. compartmentation

The enzyme catalyzing the transfer of amino group to form a double bond will be classified under....

Lyases

Km

Michaelis constant. Substrate concentration at half the maximum velocity. Smaller Km = higher affinity to substrate and ES formation

Specificity constant

High SC = low Km and high affinity = high kinetic efficiency (turnover number)

What are the most abundant molecules in nature?

Carbohydrates. Major components: C, H, O

General chemical formula for carbohydrates:

Cn(H20)n

Clockwise rotation: +, D

Counterclockwise rotation: -, L

Reaction order: 1 molecule, 1st order

a

Reaction order: 2 molecule, 2nd order

2a (unimolecular) or 2O (unimolecular) or 2(a+b) (bimolecular). NOT O2

Pseudo first order reaction

1 molecule + H2O - second order reaction behaving like first order

Uncompetitive inhibitor can only bind to...

ES complex

position of hydroxyl group on carbon 1 determines...

a or B anomer. Down is alpha

Mutarotation

a and B forms of monosaccharides can easily be interchanged when dissolved in water. Produces equilibrium mixture of a and B forms

Oxidation of aldehyde group...

Aldonic acid

Oxidation of terminal CH2OH group (not aldehyde)

Uronic acid

Oxidation of both aldehyde and terminal CH2OH group...

Aldaric acid

Reduction of aldehyde and ketone group yield..

sugar alcohols. Ex: reduction of D-Glucose yields D-Glucitol/D-Sorbitol

Monosaccharides are linked together to form disaccharide glycoside with....

glycosidic linkages

Glucose, also called Dextrose

Eyes and brain rely heavily on this source of energy

Fructose, also called Levulose

Present in large quantity in fruits and semen

Galactosemia

Lack of enzyme required for metabolism of galactose. Can cause mental retardation and cataracts and liver damage

Disaccharides

Maltose, Lactose, Cellobiose, Sucrose

lactose reducing or nonreducing

reducing

Maltose and cellobiose...

do not exist freely in nature

Maltose

Glucose + Glucose, a-1,4 glycosidic linkage. Intermediate product of starch hydrolysis

Cellobiose

Glucose + Glucose. B-1,4 glycosidic linkage

Sucrose reducing or nonreducing

Non-reducing

Amylose - linear

Glycogen & amylopectin - branched

Amylose: a-1,4 glycosidic

Amylopectin: a-1,4 and a-1,6 glycosidic linkages

Glycogen is found majorly in...

liver and muscle cells

D(-) prefix on monosaccharide means...

Its molecular arrangement is similar to D-Glyceraldehyde and it rotates light anticlockwise

D-Glucitol (D-Sorbitol) is formed from D-Glucose as a result of ....

Reduction

Oxidation of aldehyde group in D-Glucose forms....

Gluconic acid

Level of increased branching:

Amylose < Starch < Glycogen

Three stages of catabolism

1. Stage 1: Proteins digested to their fundamental parts (amino acids, sugars, fatty acids).
2. Stage 2: Further reduced to form Acetyl CoA.
3. Stage 3: Acetyl CoA is completely oxidized to form CO2 and water through the CAC and ETC.

A significant amount of energy is produced when electrons move from NADH to oxygen during

electron transport chain

Glycogenesis and glycogenolysis are controlled by three hormones:

Insulin, glucagon, and epinephrine. ALL of these are mediated by secondary messenger molecule Cyclic AMP

when glucose molecules enter cells, they are phosphorylated

Phosphorylation is catalyzed by hexokinase in the presence of ATP-Mg2+ complex (co-substrate)

Fate of pyruvate

Aerobic conditions: Pyruvate converted to Acetyl CoA then goes through the CAC to form CO2.
Anaerobic conditions: Pyruvate to lactic acid with formation of NAD . Alcohols are produced in yeast & bacteria

Regulation of glycolysis:

1. Hexokinase is inhibited by Glucose-6-phosphate.
2. PFK-1 is activated by Fructose-2,6-biphosphate and fructose-6-phosphate, and AMP. Inhibited by Citrate, ATP
3. Pyruvate kinase is activated by Fructose 1,6-biphoaphate, AMP and inhibited by Acetyl coA and ATP

Glucagon and glycolysis:

inhibits synthesis of fructose-2,6-biphosphate

Insulin and glycolysis:

Promotes synthesis of fructose-2,6-biphosphate

End product of first stage of glycolysis

2 GAD-3-P

Enzymes that play role in regulation of glycolytic pathway

Hexokinase, PFK-1, Pyruvate kinase

Mechanism of regulation of gluconeogenesis

4 enzymes

Citrate synthase

Stimulated by substrates acetyl coa and oxaloacetate.
Inhibited by citrate and succinyl coA, NADH and ATP

Isocitrate dehydrogenase ***primary regulator of CAC***

Stimulated by ADP and NAD.
Inhibited by NADH and ATP

a-ketoglutarate dehydrogenase

Stimulated by low conc. NADH and inhibited by high concentration NADH

The process in which oxygen is used as final electron acceptor

aerobic respiration

Components of ETC are located....

inner mitochondrial membrane. Organized in four complexes

Complex 1

NADH dehydrogenase complex. Transfers e- from NADH to UQ. FMN to FMNH2, then to iron sulfur centers and eventually UQ

Complex 2

Succinate dehydrogenase. Transfers electrons from succinate to UQ

Complex 3

Cytochrome bc1 complex. Transfers electrons from reduced coenzyme Q (UQH2) to cyt C

Complex 4

Cytochrome oxidase. Reduction of Oxygen to form H2O. Contains copper

Antimycin inhibits....

Cyt b (complex 3)

Rotenone and Amytal inhibit...

NADH dehydrogenase (Complex 1)

CO inhibits...

cyt oxidase (complex 4)

oxidative phosphorylation

Process by which the energy generated by the ETC is conserved by the phosphorylation of ADP to yield ATP

As electrons pass through the ETC, protons from the matrix are transported...

to the intermembrane space. create proton gradient between the matrix and intermembrane space

How many molecules of NADH are generated during CAC?

3

How many molecules of glucose are generated from one molecule of glucose during CAC?

2, transport process is 1 so 1 net

Lipid classes:

1. Fatty acids
2. Triacylglycerols
3. Wax esters
4. Phospholipids (phosphoglycerides & sphingomyelin)
5. Sphingolipids
6. Isoprenoids

Fatty acids

Naturally occurring ones are usually cis.

Triacylglycerols

Esters of glycerol with three fatty acid molecules. Neutral fats. Less oxidized than glycogen, so they release more energy. They also take up much less space. Poor conductor of heat provides insulation in low temperatures

Sphingolipids

Ceramides (precursors for glycolipids). Found in nerve cells and cell membranes

Isoprenoids

Terpenes and steroids

mixed terpenoids

Vitamin E, UQ, Vitamin K, cytokinins

Saturated fatty acids are likely to form solids because they have a higher melting point.

Unsaturated fatty acids have lower melting point because they do not pack easily because of their double bonds

Trans unsaturated fatty acids behave like saturated fatty acids because of

configuration. They are able to bend and pack. In cis form, this bending is inhibited

When triacylglycerols are esterified, what happens?

Neutralizes the charges

Glycolipids

Bind to bacterial toxins, bacteria, and plasma membranes

Lipoproteins

Blood plasma, transports lipid molecules like triacylglycerols, phospholipids, cholesterol from one organ to anotherLip

Lipid-soluble antioxidants

Carotenoids. Found in lipoproteins

Triacylglycerols are digested in small intestine by..

pancreatic lipase. forms fatty acids and monoacylglycerol

Monoacylglycerols are transported across the plasma membrane of intestinal wall and converted to triacylglycerols

Glucagon and epinephrine bind to initiate lipolysis

Carnitine

Transports acetyl CoA into the matrix

Lipogenesis precursors

Glyceraldehyde-3-Phosphate and dihydroxyacetone phosphate

Fate of glycerol after lipolysis

transported to liver to form glucose or a lipid