Biochemistry General Principles Enzymes and Energy : Biochemistry General Principles Enzymes and Energy Marc Imhotep Cray, M.D.
Lecture Objectives : Lecture Objectives To build upon the inorganic and organic chemistry concepts currently being taught/learned in with a preview of the biochemical concepts that will be introduce in detail during subsequent potions of this block
To introduce the module 0 student enzymes and energy
To introduce the module 0 student to bioenergetics definitions and classification
Slide 3 : Enzymes and Energy
Enzymes : Enzymes Increase rate of chemical reactions.
Most enzymes are proteins with diverse structure.
Functionally are biological catalysts:
Chemicals that increases the rate of a reaction.
Are not changed at the end of the reaction.
Do not change the nature of the reaction or final result.
Lower the activation energy required.
Amount of energy required for a reaction to proceed.
Enzymes (continued) : Enzymes (continued)
Mechanism of Enzyme Action : Mechanism of Enzyme Action Ability of enzymes to lower activation energy due to structure.
Each type of enzyme has has a highly-ordered, characteristic 3-dimensional shape (conformation).
Ridges, grooves, and pockets lined with specific amino acids.
Pockets active in catalyzing a reaction are called the active sites of the enzyme.
Mechanism of Enzyme Action (continued) : Mechanism of Enzyme Action (continued) Substrates have specific shapes to fit into the active sites (lock-and-key model):
Substrate fits into active sites in enzyme.
Perfect fit may be induced:
Enzyme undergoes structural change.
Enzyme-substrate complex formed, then dissociates.
Products formed and enzyme is unaltered.
Naming of Enzymes : Naming of Enzymes Enzyme name ends with suffix “-ase.”
Classes of enzymes named according to their activity or “job category.”
May specify both the substrate of the enzyme and job category.
Different organs may make different enzymes (isoenzymes) that have the same activity.
Differences in structure do not affect the active sites.
Control of Enzyme Activity : Control of Enzyme Activity Rate of enzyme-catalyzed reactions measured by the rate substrates are converted to products.
Factors influencing rate:
Temperature.
pH.
[cofactors and coenzyme].
[enzyme and substrate].
Stimulatory and inhibitory effects of products of enzyme action.
Effect of Temperature : Effect of Temperature Rate of reaction increases as temperature increases.
Reaction rate plateaus, slightly above body temperature (37o C).
Reaction rate decreases as temperature increases.
Enzyme denature at high temperatures.
pH : pH Each enzyme exhibits peak activity at narrow pH range (pH optimum).
pH optimum reflects the pH of the body fluid in which the enzyme is found.
If pH changed, so is no longer within the enzyme range; reaction will decrease.
Cofactors and Coenzymes : Cofactors and Coenzymes Needed for the activity of specific enzymes.
Cofactor:
Attachment of cofactor causes a conformational change of active site.
Participate in temporary bonds between enzyme and substrate.
Coenzymes:
Organic molecules derived from H20 soluble vitamins.
Transport H+ and small molecules from one enzyme to another.
Enzyme Activation : Enzyme Activation Enzymes may be produced in an inactive form.
In pancreas, digestive enzymes are produced as inactive zymogens, which are activated in lumen of intestine.
Protects against self-digestion.
In liver cells, enzyme is inactive when produced and is activated by addition of phosphate group.
Phosphorylation/dephosphorylation:
Activation/inactivation of an enzyme.
Substrate Concentration : Substrate Concentration At a specific [enzyme], rate of product formation increases as the [substrate] increases.
Plateau of maximum velocity occurs when enzyme is saturated.
Additional [substrate] does not not increase reaction rate.
Reversible Reactions : Reversible Reactions Some enzymatic reactions are reversible.
Both forward and backward reactions are catalyzed by same enzyme.
H20 + C02 H2C03
Law of mass action:
Principal that reversible reactions will be driven from the side of the equation where concentration is higher to side where concentration is lower. ca biochemistry
Metabolic Pathways : Metabolic Pathways Sequence of enzymatic reactions that begins with initial substrate, progresses through intermediates and ends with a final product.
End-Product Inhibition : End-Product Inhibition Negative feedback inhibition.
One of the final products in a divergent pathway inhibits the activity of the branch-point enzyme.
Prevents final product accumulation.
Results in shift to product in alternate pathway.
Inborn Errors of Metabolism : Inborn Errors of Metabolism Inherited defect in a gene for enzyme synthesis.
Quantity of intermediates formed prior to the defect increases.
Final product formed after the defect decreases, producing a deficiency.
Slide 19 : Bioenergetics
Bioenergetics : Bioenergetics Flow of energy in living systems obeys:
1st law of thermodynamics:
Energy can be transformed, but it cannot be created or destroyed.
2nd law of thermodynamics:
Energy transformations increase entropy (degree of disorganization of a system).
Only free energy (energy in organized state) can be used to do work.
Systems tend to go from states of higher free energy to states of lower free energy.
Endergonic and Exergonic Reactions : Endergonic and Exergonic Reactions Endergonic:
Chemical reactions that require an input of energy to make reaction “go.”
Products must contain more free energy than reactants.
Exergonic:
Convert molecules with more free energy to molecules with less.
Release energy in the form of heat.
Heat is measured in calories.
Coupled Reactions: ATP : Coupled Reactions: ATP Cells must maintain highly organized, low-entropy state at the expense of free energy.
Cells cannot use heat for energy.
Energy released in exergonic reactions used to drive endergonic reactions.
Require energy released in exergonic reactions (ATP) to be directly transferred to chemical-bond energy in the products of endergonic reactions.
Formation of ATP : Formation of ATP Formation of ATP requires the input of a large amount of energy.
Energy must be conserved, the bond produced by joining Pi to ADP must contain a part of this energy.
This energy released when ATP converted to ADP and Pi.
ATP is the universal energy carrier of the cell.
Oxidation-Reduction : Oxidation-Reduction Reduced:
Molecule/atom gains electrons.
Reducing agent:
Molecule/atom that donates electrons.
Oxidized:
Molecule/atom loses electrons.
Oxidizing agent:
Molecule/atom that accepts electrons.
Reduction and oxidation are always coupled reactions.
Oxidation-Reduction (continued) : Oxidation-Reduction (continued) May involve the transfer of H+ rather than free electrons.
Molecules that serve important roles in the transfer of hydrogen are NAD and FAD.
Coenzymes that function as hydrogen carriers.
Oxidation-Reduction (continued) : Oxidation-Reduction (continued)
Carbohydrate Nomenclature (I) : Carbohydrate Nomenclature (I) Carbohydrate Classes:
Monosaccharides (CH2O)n
Simple sugars, can not be broken down further;
Oligosaccharides
Few simple sugars (2-6).
Polysaccharides
Polymers of monosaccharides
Carbohydrate Nomenclature (II) : Carbohydrate Nomenclature (II) Monosaccharide (carbon numbers 3-7)
Aldoses
Contain aldrhyde
Name: aldo-#-oses (e.g., aldohexoses)
Memorize all aldoses in Figure ?
Ketoses
Contain ketones
Name: keto-#-oses (ketohexoses)
Carbohydrates : Carbohydrates Carbohydrates are the most abundant organic molecules in nature
Photosynthesis energy stored in carbohydrates;
Carbohydrates are the metabolic precursors of all other biomolecules;
Important component of cell structures;
Important function in cell-cell recognition;
Carbohydrate chemistry:
Contains at least one asymmetric carbon center;
Favorable cyclic structures;
Able to form polymers
Sterochemistry of Monosaccharides (I) : Sterochemistry of Monosaccharides (I) D,L steroisomers refers to the configuration of the highest assymmetric carbon (farthest from the carbonyl carbon):
Hydroxyl group is drawn to the right - D
Hydroxyl group is drawn to the left - L
Note that D, L assignment does not specify the sign of rotation of plane-polarized light.
D(+)-glucose is dextrorotatory D-glucose; D(-)-fructose is levorotatory D-fructose
D is the preferred configuration in nature
Sterochemistry of Monosaccharides (II) : Sterochemistry of Monosaccharides (II) Each asymmetric carbon can have 2 configurations, thus for a sugar of n carbons, there are 2(n-2) possible steroisomers. Know the following definitions:
Diastereomers
Isomers that have opposite configuration at one or more carbons but are not mirror images of each other
Enantiomers
Isomers that are mirror images
Epimers
Isomers that differ in only one carbon configuration
Examples of Stereoisomers : Examples of Stereoisomers
Cyclic Structures of Aldohexoses : Cyclic Structures of Aldohexoses Alcohols react readily with aldehydes to form hemiacetals;
Linear form of aldohexoses could undergo a similar intra-molecular reaction to form a cyclic hemiacetals;
See next slide
Cyclic Hemiacetals : Cyclic Hemiacetals a-D-glucopyranose b-D-glucopyranose Haworth
Projection Fisher
Projection
Cyclic Structures of Ketohexoses : Cyclic Structures of Ketohexoses ketones react readily with alcohols to form hemiketals;
Linear form of ketohexoses could undergo a similar intra-molecular reaction to form a cyclic hemiketals;
See next slide
Cyclic Hemiketals : Cyclic Hemiketals D-Fructose a-D-fructofuranose b-D-fructofuranose Haworth
Projection Fisher
Projection
Sugar Anomers : Sugar Anomers The formation of hemiketals and hemiacetals results in
an asymmetric carbon atom.
Isomers that differ only in their configuration about the
new asymmetric carbon are called anomers, the carbonyl
carbon is called anomeric carbon.
a-anomer has the hydroxyl group on the same side of
The oxygen at the highest numbered asymmetric carbon;
b-anomer has the hydroxyl group on the opposite side of
The oxygen at the highest numbered asymmetric carbon
Monosaccharide Structures : Monosaccharide Structures Conformation
of monosaccharide Conformation
of glucose
Sugar Derivatives : Sugar Derivatives Sugar alcohols are formed by mild reduction (with NaBH4 or similar) of carbonyl groups of sugars;
Add -itol to the name of the parent sugar
Amino sugars contain an amino group in place of a hydroxyl group. They are found in many polysaccharides (for example, chitin).
Examples of Sugar Derivatives : Examples of Sugar Derivatives Sugar Alcohols Amino Sugars,
Muramic Acid
Acetals, Ketals and Glycosides : Acetals, Ketals and Glycosides Hemiacetals and hemiketals can react with alcohols in the presence of acid to form acetals and ketals.
Pyranose and furanose forms
of monosaccharides react with
alcohols to form glycosides.
Disaccharides : Disaccharides Simplest oligosaccharides;
Contain two monosaccharides linked by a glycosidic bond;
The free anomeric carbon is called reducing end;
The linkage carbon on the first sugar is always C-1. So disaccharides can be named as sugar-(a,b)-1,#-sugar, where a or b depends on the anomeric structure of the first sugar. For example, Maltose is glucose-a-1,4-glucose.
Strutures of Disaccharides : Strutures of Disaccharides Note the linkage and reducing ends
Polysacchrides : Polysacchrides Also called glycans;
Starch and glycogen are storage molecules;
Chitin and cellulose are structural molecules;
Cell surface polysaccharides are recognition molecules.
Polysacchrides : Polysacchrides Glucose is the monosaccharides of the following polysacchrides with different linkages and banches
a(1,4), starch (more branch)
a(1,4), glycogen (less branch)
a(1,6), dextran (chromatography resins)
b(1,4), cellulose (cell walls of all plants)
b(1,4), Chitin similar to cellulose, but C2-OH is replaced by –NHCOCH3 (found in exoskeletons of crustaceans, insects, spiders)
Slide 46 : Question1: Known enzymes are
A. Catalytically active biological molecules, exceptionally proteins
B. Catalytically active proteins and RNA molecules
C. The protein portion of any catalyst
D. Catalytically active organic molecules
E. Catalytically active polysaccharides
Slide 47 : Question2: Apoenzymes are
A. The proteins which catalyze the apoptosis, programmed cell death
B. Specific substrates of the enzymes
C. Competitive inhibitors of the enzymes
D. The protein portion of an enzyme which requires a prosthetic group, coenzyme or cofactor to develop the full enzymatic activity
E. The enzymes which perform metabolic conversions of apolipoproteins
Slide 48 : Question3: Holoenzymes are
A. The proteins which perforate cell membranes causing the leakage of the cytoplasm through the developing holes and the subsequent cell death
B. Fully enzymatically active complexes of the apoenzymes with their cofactors, prosthetic groups or coenzymes
C. Holographic images of enzymes
D. Metalloproteins having an atom of holmium bound to their molecule
E. The enzymes which have a cavity for the binding of a substrate or modulator in their conformational structure
Slide 49 : Question4: Prosthetic group is
A. A substrate of the enzyme prostaglandin endoperoxide synthase
B. A specific substrate of an enzyme
C. A synonym of the term coenzyme
D. A group of biologically active metabolites of arachidonic acid, including prostaglandins and prostacyclins
E. Nonprotein component which is tightly bound to a protein, for example an enzyme
Slide 50 : Question5: What part of the NAD+ molecule directly participates in oxidation‑reduction reactions
A. Adenine
B. Nicotinamide‑attached ribose
C. Phosphate group
D. Aden ine‑aftached ribose
E. Nicotinamide
Slide 51 : Question6: What part of the FAD molecule directly participates in oxidation‑reduction reactions?
A. Adenine
B. Ribitol
C. Phosphate group
D. Isoalloxazine ring
E. Aden i ne‑attached ribose
Slide 52 : Question7: Homopolysaccharides and heteropolysaccha rides are respectively
A. Of human (homo‑) and nonhuman (hetero‑) origin
B. Containing only C,H, and 0 atoms (homo‑) and some other atoms, like N, S (hetero‑)
C. Composed of similar (homo‑) and different (hetero‑) monomers
D. Nonbranched (homo‑) and heavily branched (hetero‑)
E. Composed of sugar monomers only (homo‑) and sugar derivatives combined with sugars (hetero‑)
Slide 53 : Question8: A major difference between the structures of cellulose and glycogen is
A. Cellulose contains galactose in addition to glucose
B. Cellulose is found only in animals
C. The type of linkages between glucose residues
D. Cellulose is highly branched
E. Glycogen is less soluble than cellulose
Slide 54 : Question9: Amylose is a
A. Pancreatic enzyme responsible for the digestion of polysaccharides
B. Branched component of starch
C. Pancreatic enzyme responsible for the digestion of disaccharides
D. Unbranched component of glycogen
E. Unbranched component of starch
Slide 55 : Question10: Which of the following sugars is an epimer of galactose?
A. Glucose
B. Arabinose
C. Xylulose
D. Fructose
E. Mannose
Slide 56 : Question11: Mutarotation of glucose molecule means the conversion of
A. D‑enantiomer into L‑form B. C‑4 epimer into C‑3 epimer C.
(x‑D‑glucopyranose into (x‑D‑glucofuranose
D. C‑4 epimer into C‑2 epimer
E. Cyclic a anomer into P form
Slide 57 : Question12: The main difference between the two forms of starch, amylopectin and amylose, is
A. Amylopectin contains glucose in (x‑(1,4) linkages and amylose contains only 0‑(1,4)
B. Amylopectin occurs in animals and amylose occurs in plants
C. Amylopectin functions to provide mechanical rigidity to plants and amylose is a storage form of glucose
D. Amylopectin contains glucose in (x‑(1,4) and (x‑(1,6) linkages, while amylose contains only (x‑(1,4)
E. Amylopectin contains glucose and galactose and amylose only contains glucose
Answers : Answers 1. B: Catalytically active proteins and RNA molecules
2. D: The protein portion of an enzyme which requires a prosthetic group, coenzyme or cofactor to develop the full enzymatic activity
3. E~ Fully enzymatically active complexes of the apoenzymes with their cofactors, prosthetic groups or
coenzymes
4. E: Nonprotein component which is tightly bound to a protein, for example an enzyme
5. E: Nicotinamide
6. D: Isoalloxazine ring
Slide 59 : 7. C: Composed of similar (homo‑) and different (hetero‑) monomers
8. C: The type of linkages between glucose residues
9. E: Unbranched component of starch
10. A: Glucose
11. E: Cyclic (x anomer into P form
12. D: Amylopectin contains glucose in (x‑(1,4) and (x‑(1,6) linkages, while amylose contains only a‑(1,4)