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L28L28--11
ChE
400
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activ
e Pr
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gine
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040
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Enzyme Catalysis & BiotechnologyEnzyme Catalysis & Biotechnology
Bovine Pancreatic RNase A
L28L28--22
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400
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Biochemistry, Life, and all that
BiochemistryBiochemistry - studies biological (living) species in chemical terms- compositions and structure of biochemical molecules, trying to understand their
functions at a molecular level.
General observations on biochemical molecules- generally very large: molecular weight ~ O(1,000) – O(1,000,000) amu
- generally rather simple composition: mostly C, O, H as their main building blocks and relatively few other atoms (such N, P, S) in their functional groups
- generally rather complex structures: specific structure is crucial to their highly specialized functions in biological processes.
All life processes on earth require energy (processes of bio-molecule synthesis are endothermic), which is obtained indirectly from solar energy through plant photosynthesis.
A brief word about biochemistry……traditionally, chemical engineers used organic and inorganic chemistry (along with some physics, lots of math, and other fancy things) to “make stuff”. Anything “bio” was regarded as beyond the reach of industrial activities and/or sufficiently uninteresting. This has changed completely in the past few decades.This has changed completely in the past few decades.
L28L28--33
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400
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Photosynthesis and RespirationPhotosynthesisPhotosynthesis and respirationrespiration as complementary processes in the living world. Photosynthesis uses the energy of sunlight to produce sugars and other organic molecules. These molecules serve as food for other organisms. Many of these organisms carry out respiration, a process that uses O2 to form CO2. In the process, the organisms that respire obtain the chemical bond energy that they need to survive. The first cells on the earth are thought to have been capable of neither photosynthesis nor respiration. However, photosynthesis must have preceded respiration on the earth, since there is strong evidence that billions of years of photosynthesis were required before O2 had been released in sufficient quantity to create an atmosphere rich in this gas. (The earth's atmosphere presently contains 20% O2.)
L28L28--44
ChE
400
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Maintaining Order…Cells must maintain highly organized, low-entropy state at the expense of free energy.
Cells cannot use heat for energy (cells are very heat-sensitive!).
Energy released in exergonicreactions used to drive endergonic reactions.
Require energy released in exergonicreactions (ATP) to be directly transferred to chemical-bond energy in the products of endergonicreactions.
Endergonic/exergonic refer to free energy changes (ΔG). Endothermic and exothermic refer to ΔH. For many chemical reactions, entropy contributions are relatively small, so chemists usually refer to ΔH.For many biological reactions, entropy contributions are significant, so biochemists usually talk about ΔG.
L28L28--55
ChE
400
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ATP – Major Energy CarrierFormation of ATP requires the input of a large amount of energy, stored in the bond energy by joining Pi to ADP. This energy released when ATP converted to ADP and Pi.
ATP is the universal energy carrier of the cell.
ΔH ~ 30 kJ/molΔH ~ 30 kJ/mol
+ H2O
L28L28--66
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400
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Metabolism: GlycolysisA bag of sugar can be stored for years A bag of sugar can be stored for years
with little conversion to COwith little conversion to CO22 and Hand H22OO
HoweverHowever: this conversion is basic to life : this conversion is basic to life --> need to accelerate it!> need to accelerate it!
Mother Nature’s Solution:Mother Nature’s Solution:
Glycolysis – the break-down of glucose to pyruvate, catalyzed by enzymes
• Embden-Meyerhof Pathway:universal pathway - occurs in essentially all organisms
• overall net gain of 2 ATP
L28L28--77
ChE
400
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The 10 Steps of Glycolysis – I
L28L28--88
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400
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The 10 Steps of Glycolysis - II
L28L28--99
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400
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The 10 Steps of Glycolysis - III
L28L28--1010
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400
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Enzymes: Why?Living organisms must be able to carry out chemical reactions which are
thermodynamically highly unfavorable
– Break and form covalent bonds
– Move large structures
– Make complex three dimensional structures
– Regulate gene expression
They do so through enzyme catalysisenzyme catalysis.
Enzymes have immense importance in a wide variety of fields:
• Genetic diseases are frequently defects in enzymes or increased/decreased levels of enzymes
• Many modern drugs exert effects by interacting with enzymes
• Used in food processing and in chemical industry
• Enzyme inhibitors are a foundation of biological weapons (as well as of some of the counter-measures)
Enzymes have immense importance in a wide variety of fields:
• Genetic diseases are frequently defects in enzymes or increased/decreased levels of enzymes
• Many modern drugs exert effects by interacting with enzymes
• Used in food processing and in chemical industry
• Enzyme inhibitors are a foundation of biological weapons (as well as of some of the counter-measures)
L28L28--1111
ChE
400
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Enzymes, Proteins and Amino AcidsEnzymes are proteins that act as catalysts for biochemical reactEnzymes are proteins that act as catalysts for biochemical reactionsions.
Proteins are very large biomolecules present in living cells (~50% dry wt of our body).
All proteins are composed of the same building blocks - αα--amino acidsamino acids.
H
R
+H3N-C-C-O-
OH
R
H2N-C-C-OHO
or “zwitter-ion”(at neutral pH)
non-ionicform
H
R
H2N-C-C-OHO
+ H2OH
R’
H2N-C-C-OHO
H
H
R
H2N-C-C-N-C-C-OH
O OH
R’
amide group
+ =
α-amino acids are linked by amide groups, which are formed in a condensation reaction between the acid and amine groups of two amino acids:
This bond is also referred to as ‘peptide bond’, and the resulting molecules are ‘peptides’.
L28L28--1212
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400
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Formation of a Peptide Bondgeneral reaction scheme:general reaction scheme: example:example:
Amino AcidAmino Acid PeptidePeptide Poly-PeptidePoly-Peptide Protein (e.g. Enzymes)Protein (e.g. Enzymes)
Peptides, Polypeptides, and Proteins (among them: Enzymes) are ‘Peptides, Polypeptides, and Proteins (among them: Enzymes) are ‘amino acid polymers’! amino acid polymers’!
L28L28--1313
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400
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The 20 Amino Acids Found in Proteins
L28L28--1414
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400
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Names & Types of EnzymesEnzyme names (mostly) end in Enzyme names (mostly) end in ––asease- identifies a reactant: sucrase - reacts sucrose, lipase - reacts lipid
- common names of digestion enzymes still use –in: pepsin, trypsin
- describes function of enzyme:
Class Reactions catalyzed
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
ClassClass Reactions catalyzedReactions catalyzed
OxidoreductasesOxidoreductases
TransferasesTransferases
HydrolasesHydrolases
LyasesLyases
IsomerasesIsomerases
LigasesLigases
L28L28--1515
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Learning Check E1Match the type of reaction with the enzymes:
(1) aminase (2) dehydrogenase
(3) Isomerase (4) synthetase
( ) Converts a cis-fatty acid to trans.
( ) Removes 2 H atoms to form double bond
( ) Combine two molecules using ATP
( ) Adds NH3
L28L28--1616
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400
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Enzyme Structure
The threeThe threecrucial for their functionality.crucial for their functionality.
Four hierarchical levels of enzyme structure are Four hierarchical levels of enzyme structure are distinguished: distinguished: primary, secondary, tertiary and quaternary.primary, secondary, tertiary and quaternary.
--dimensional structure of enzymes is dimensional structure of enzymes is
L28L28--1717
ChE
400
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Enzymes: Primary Structure
Primary structure: sequence of amino acids
glycine (G)
alanine (A)
valine (V) leucine (L)
serine (S) threonine (T)
cysteine
methionine (M)
phenylalanine (F) tyrosine (Y)
proline
isoleucine (I)
lysine (K)
tryptophan (W)
histidine (H)
asparticacid (D)
glutamicacid (E)
aspargine (N) glutamine (Q)
arginine (R)
3++2
: KVFGRCELAAAMKRHGLDNY…
L28L28--1818
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400
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Primary Structure of Bovine InsulinFirst protein to be fully sequenced;Fred Sanger, 1953. For this, he won his first Nobel Prize (his second was for DNA sequencing).
L28L28--1919
ChE
400
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Enzymes: Secondary Structure
Alpha-Helix Beta-Sheet
Secondary structure: packing of amino acids (helix, sheet),i.e. the spatial arrangement of the ‘back-bone’ of the enzyme (without special consideration of side groups).
L28L28--2020
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400
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Enzymes: Tertiary Structure
ribonuclease Aloop(non-repeating coil structure)
alpha-helix beta-sheetTertiary structure: cross-linking and 3D conformation,i.e. complete spatial arrangement of one enzyme
L28L28--2121
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400
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Enzymes: Quaternary StructureQuaternary structure: enzyme oligomers, i.e. spatial arrangement of enzymes (and other peptides) which consist of several sub-units.
L28L28--2222
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400
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Enzyme Structure: RecapFour hierarchical levels of enzyme structure:Four hierarchical levels of enzyme structure:
Primary structure:sequence of amino acids (1D)
Primary structure:sequence of amino acids (1D)
Secondary structure:spatial arrangement of backbone (2D)
Secondary structure:spatial arrangement of backbone (2D)
Tertiary structure:detailed spatial conformation of one enzyme (3D)
Tertiary structure:detailed spatial conformation of one enzyme (3D)
Quaternary structure:spatial conformation of multiple enzymes (‘oligomers’)
Quaternary structure:spatial conformation of multiple enzymes (‘oligomers’)
L28L28--2323
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400
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Enzyme Action: Models
‘‘Lock and Key’ ModelLock and Key’ Model
An enzyme binds a substrate in a region called the active site
Only certain substrates can fit the active site
Amino acid R groups in the active site help substrate bind
Induced Fit ModelInduced Fit Model
Enzyme structure flexible, not rigid
Enzyme and active site adjust shape to bind substrate
Increases range of substrate specificity
Shape changes also improve catalysis during reaction-> transition-state like configuration
In each case, an enzyme-substrate complex is formed, the respective bonds in the substrate are formed or broken
(i.e. the reaction occurs), and the product(s) are released:E + S <=> ES <=> E + P
L28L28--2424
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400
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‘Lock and Key” Model
(A) The folding of the polypeptide chain typically creates a crevice or cavity on the proteinsurface. This crevice contains a set of amino acid side chains disposed in such a way thatthey can make noncovalent bonds only with certain ligands.
(B) Close-up view of an actual binding site showing the hydrogen bonds and ionic interactions formed between a protein and its ligand (in this example, cyclic AMP is the bound ligand).
L28L28--2525
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400
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Induced Fit Model
Induced Conformational Change in Hexokinase
L28L28--2626
ChE
400
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Enzyme-Substrate Interaction