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1.

Application of enzyme :
2. Lipase: Enhancing flavor development and shortening the time for cheese ripening. Production
of specialty fats with improved qualities. Production of enzyme-modified cheese/butter from cheese
curd or butterfat.
3. Papain: Used as meat tenderizer. Used in brewing to prevent chill-haze formation by digesting
proteins that otherwise react with tannins to form insoluble colloids.
4. Microbial proteases: Processing of raw plant and animal protein. Production of fish meals,
meat extracts, texturized proteins, and meat extenders.
5. Pectinase: Treatment of fruit pulp to facilitate juice extraction and for clarification and filtration
of fruit juice.
6. Lactase: Additive for dairy products for individuals lacking lactase. Breakdown of lactose in
whey products for manufacturing polyactide.
7. Cellulase: Conversion of cellulose waste to fermentable feedstock for ethanol or single-cell
protein production. Degradation of cell walls of grains, allowing better extraction of cell contents
and release of nutrients.

2. Coenzyme’s role in enzyme catalyzed reaction :

Non protein, also bind to active site but not considered as substrate. Function as intermadiate carrier
of electron, specific atoms/ functional groups that are transfered in the overal reaction

The active site also contains functional groups that participate directly in the reaction .The
functional groups are donated by the polypeptide chain or by coenzymes. As the substrate binds, it
induces conformational changes in the enzyme that promote further interactions between the
substrate molecules and the enzyme functional groups.

3.Clarify the structure and properties of active site


Structure of active sites
• The active site takes up a relatively small part of the total volume of an enzyme
• The active site is a three dimentional entily
• Substrates are bound to enzymes by multiple weak attraction
• Active sites are clefts or crevices
• Functional residues in enzyme binding directly to substrate to form or break down the bonding
in substrates to produce products

Properties of active sites

 Many different functional residues of amino acids, water in bonding, metal ions, functional
residues of coenzyme
4. Write down 6 categories of enzymes. Discuss and focus first 3 groups
Oxidoreductase - Transferases - Hydrolases - Lyases – Isomerases - Ligases
i. Oxidoreductase
 Oxidoreductase catalyze oxidation-reduction reactions.
 Subclasses of this group include
o Dehydrogenase
- Catalyze the reaction in which H+ from substrate transfering to NAD+, NADP+, FAD, FMN
 These enzymes can be found some first stages of ETC
-The reactions: H from NADH, NADPH, FADH2, FMNH2, can be transferred to substrate and
reduce the substrates
 Catalyze the synthesis reaction
 Alcoholdehydrogenase
CH3CH2OH + NAD+  CH3CHO + NADH + H+
 important role in alcohol fermentation
Glutamatedehydrogenase

L-glutamic + H2O + NAD+  -ketoglutaric + NH3 + NADH + H+


 N from soil to plant and microorganism by absorbing NH3

o Reductase
Catalize the process in which electron can be transferred to Oxygen and then Oxygen can combine
with proton
4 Ferocytochrom c + O2 + 4H+ = 4 Fericytochrom c + 2H2O
o Oxygenase
Catalyze oxido-reduction reactions in which Oxygen can combine with substrate to form functional
groups as -OH, -COOH
o Peroxydase
- Including peroxydase and Catalase
- Coenzyme is hem
- Catalyze organic substrates in the presence of H2O2
Peroxydase:Donating substrate + H2O2 = oxidized substrate + H2O
Catalase: H2O2 + H2O2 = O2 + 2H2O
ii. Transferases
Transferases catalyze reactions that involve the transfer of groups from one molecule to another
such as amino, carboxyl, carbonyl, methyl, phosphoryl, and acyl (RC=O) and the enzyme names
often go with trans such as transcarboxylase, transmethylase, and transaminases
iii. Hydrolases
 Hydrolases catalyze reaction in which the cleavage of bonds is accomplished by adding water
 Hydrolases include the esterases, phosphatase, and peptidase

5. What do you know enzyme kinetic? Write down the Michaelis-Menten equation and
discuss the Vmax and Km.
6. Can you recommend the enzyme source?
-In the past, enzymes were being produced strictly from animals (liver/pancreas) but not very
stable at the low pH (acidic) environment of the stomach  denature before do the job
-After that Plant enzymes were used. These animal-friendly enzymes are much more stable
under low pH conditions, such as inside the stomach, and temperature changes don't seem to
affect them as much.
-Microbial enzymes have since come along and provide for numerous enzymes that perform
multiple body functions. Microbial enzymes are extracted from fermented bacteria or fermented
fungal organisms.
8. What do you know about glycolysis, focus on structure of intermediate enzymes, NADHs
and ATP?
-Glycolysis harvests chemical energy by oxidizing glucose to pyruvate
-In a eukaryotic cell, glycolysis occur outside the mitochondria in cytosol
-The pathway of glycolysis consists of 10 steps, each is catalyzed by a specific enzyme.
This is divided into 2 phases: the energy investment phase (first 5 steps) and the energy payoff
phase (final 5 steps)
-During the energy investment phase, the cell spends ATP to phosphorylate the fuel molecules and
NAD+ is reduced to NADH by oxidation of food
-Structure of intermediate enzymes:

Hexokinase Is a homodimer
-Each subunit is made of 2 globular domain linked by an α
helix
-The subdomains are composed of 2 segments of β sheet
-The active sites are sandwiched between β sheets. The active
site has a space to bind both glucose and ATP
Phosphoglucose Isomerase -Is a homodimer
-Is composed of 2 globular subunits that embrace each other
with flanking a helical “arms”
-Each subunit is composed of one mixed and one parallel β
sheet which separated by a central bundle of α helices
-The active site are located symmetrically at the interface
between 2 subunits

Phospho-fructokinase Exists as a tetramer in solution


-Is a dimer of dimers
-Each subunit contains 319 amino acids that form 2 domains.
The larger binds the substrate ATP and the smaller binds
other substrate, fructose-6-phosphate
-Each domain is a β barrel
Aldolase Is a tetramer of identical subunits
-Each subunit is composed of αβ barrel surrounded by β
helices
-The active site is located at one end of β barrel
Triose phosphate isomerase -Is a dimer made from 2 globular subunits
-Each subunit is composed of a central β barrel surrounded by
α helices
Glyceraldehyde-3-phosphate -Is a tetramer
dehydrogenase -Each identical subunit is composed of 2 extended β sheets
which supported by 3 α helices
Phosphoglycerate kinase -Each subunit is composed of 2 subdomains made of a central
β sheet which is surrounded by a bundle of α helices
-The active site is divided between 2 domains. One binds to
ADP and one binds to 1.2-biphosphoglycerate

Phosphoglycerate mutase Each subunit is composed if 2 subdomains made from a


central β sheet which is surrounded by α helices
-The active site is located between 2 subdomains
Enolase -Is a homodimer
-Each subunit is a β barrel surrounded by α helices
-The interface between 2 subunits is a flat surface
-The active sites are located within a cavity close to center of
each subunit
Pyruvate kinase Contains a “cupped hand” domain made from 4 separate
segments of β sheet surrounded by α helices
-The active site is located inside the cup

9. What do you know about CAC (Krebs cycle), focus on structure of intermediate enzymes,
CO2, NADHs, FADH, and ATSs?
The central roles of the CAC:
– To increase the ATP-producing potential of the cell by generating reduced electron carriers
(NADH)
– To provide the cell with a variety of metabolic precursors for biosynthesis
- In prokaryotic, CAC takes place in cytosol while in eukaryotic, CAC takes place within the
mitochondria matrix
-Both prokaryotic and eukaryotic use CAC to help meet their energetic and molecular needs
CAC is catabolic: molecules are broken down to serve energy needs of the cell
-The main purposes of CAC:
+Increase the cell’s ATP-producing potential by generating a reduced electron carriers such as
NADH and reduced ubiquinone
+Provide the cell with a variety of metabolic precursors
-Intermediates in CAC:
+Citrate +Succinate
+Isocitrate +Fumarate
+Α-ketoglutarate +Malate
+Succinyl-CoA +Oxaloacetate
10.Metabolism

-Metabolism : Metabolism is all the chemical reactions that occur in living organisms
the sum of the chemical changes that convert nutrients intro energy and the complex finished products of cells
Basic function:
+ Obtainenergy from fuel molecules or sunlight
-Metabolism is a central theme in biochemistry. It keeps cells and organisms alive by:

+giving them the energy to carry on

+the building blocks required for growth and propagation.

-The metabolism can be divided into: catabolic and anabolic reactions

- Two kinds of metabolic reactions:

– Catabolism = breakdown of large molecules into simple ones to produce energy (release energy)
degreadative pathways
– Anabolism = build large molecules from simple molecules. (requires energy input)
biosynthetic pathways
+The term catabolic means the same as degradative, the key functions of catabolic reactions are:
Decomposition of large complex molecules into small molecules
1. accumulation of energy in the form of ATP, +Degredative +Oxidative

2. regeneration of reducing power (NADPH), and Energy liberated +Converge


3. production of building blocks for anabolic metabolism.

+anabolic metabolism Large complex organic molecules are constructed from small molecules
+ Biosynthetic +Reductive + Energy required +Diverging
1. small molecules and building blocks that are not sufficiently available in the food

2. macromolecules, in particular proteins and nucleic acids

3. Apart from building blocks and ATP, anabolic reactions also require a good deal of reducing
power in the form of NADPH.

-NADPH is the reduced form of NADP+. NADP+ differs from NAD+ in the presence of an
additional phosphate group on the 2' position of the ribose ring that carries the adenine moiety.

Metabolism role in life

A large share of the substrates broken down in catabolism are being used for producing ATP. ATP
is used for nearly every energy-requiring task in cell biology. This includes

1. cell motility, particularly in muscle cells,

2. active transport across membranes, e.g. Na+/K+-ATPase and other ion pumps. Ion pumps are
largely responsible for the conspicuous energy requirements of brain and kidneys,

11. Discuss and exemplify the differences b/w anabolism and catabolism where possible

Anabolism Catabolism
Large molecules are constructed from small Decomposition of large complex molecules
molecules (build up) into small ones
Enery required Energy liberated
Reductive Oxidative
Biosynthetic Degradative
Diverging Converging

Eg:

12. Focus and discuss the energy-generating pathways of carbohydrates metabolism


Carbohydrate metabolism refers to the production, storage and use of carbohydrates within
organisms.
The energy-generating pathways of carbohydrates metabolism contains 3 major pathways:
Glycolysis, Kreb cycle and Electron transport chain..
- During glycolysis, each glucose molecule is broken down into two molecules of the compound
pyruvate.
- The pyruvate crosses the double membrane of the mitochondrion to enter the matrix, where the
Krebs cycle decomposes it to carbon dioxide.
- NADH or FADH2 transfers electrons from molecules undergoing glycolysis and the Krebs cycle
to electron transport chains, which are built into the inner mitochondrial membrane.
The electron transport chain converts the chemical energy to a form that can be used to drive
oxidative phosphorylation, which accounts for most of the ATP generated by cellular respiration.
- A smaller amount of ATP is formed directly during glycolysis and the Krebs cycle by substrate-
level phosphorylation.

Respiration is a cumulative function of 3 metabolic stages:


(1) Glycolysis – cytosol: In a eukaryotic cell, glycolysis occurs outside the mitochondria in the
cytosol.
Glycolysis, begins the degradation by breaking: glucose = two molecules pyruvate
 Stages of glycolysis
1. Stage one (the energy requiring stage):
a) One molecule of glucose is converted into two molecules of glycerosldhyde-3-phosphate.
b) These steps requires 2 molecules of ATP (energy loss)
2. Stage two (the energy producing stage ):
a) The 2 molecules of glyceroaldehyde-3-phosphate are converted into pyruvate (aerobic
glycolysis) or lactate (anaerobicglycolysis
(.b) These steps produce ATP molecules (energy production).

(2) The Krebs cycle - mitochondrial matrix : The Krebs cycle and the electron transport chains are
located inside the mitochondria
Decomposing a derivative of pyruvate to CO2

(3) The electron transport chain and oxidative phosphorylation


The electron transport chain accepts electrons from the breakdown products of the first two stages
(usually via NADH) and passes these electrons from one molecule to another
-The energy released at each step of the chain is stored in a form the mitochondrion can use to
make ATP.
- This mode of ATP synthesis is called oxidative phosphorylation because it is powered by the
redox reactions that transfer electrons from food to O2.
- Oxidative phosphorylation accounts for almost 90% of the ATP generated by respiration
- A smaller amount of ATP is formed by substrate-level phosphorylation when an enzyme
transfers a phosphate group from a substrate molecule to ADP. "Substrate molecule" here refers
to an organic molecule generated during the catabolism of glucose.

glucose = CO2 + H2O + 38 molecules of ATP


13. What is biochemistry and its covering scope as well as its apps in life science?
-Biochemistry is the study of chemical processes within and relating to living organisms. By
controlling information flow through biochemical signaling and the flow of chemical energy
through metabolism, biochemical processes give rise to the complexity of life. Much of
biochemistry deals with the structures, functions and interactions of biological macromolecules.
The chemistry of the cell also depends on the reactions of smaller molecules and ions.
-The scope of biochemistry is to understand chemical structures/function of biological molecules,
interaction and organization of different molecules within individual cells and whole biological
systems, and bioenergetics. Therefore opens up the scopes in the field biotechnology,
pharmacology, medicine, dentistry, agriculture, forensics, anthropology, environmental
sciences..etc
- Biochemistry: foundation for understanding all biological processes. It has provided explanations
for the mechanisms and developments of living cells as well as causes of many diseases in humans,
animals and plants

14. Show your understanding about energy-generating pathways of carbohydrate metabolism


including glycolysis?
*Carbohydrate metabolism refers to the production, storage and use of carbohydrates within
organisms. Carbohydrates all consist of carbon, hydrogen and oxygen (CnH2nOn), yet not all forms
of carbohydrate can be metabolised.
The primary example of a carbohydrate that is used almost universally within living organisms is
glucose which is a monosaccharide. However, larger molecules (disaccharides, oligosaccharides
and polysaccharides) are also metabolized within our bodies.

*Glycolysis
- Occurs in cytoplasm
- Is an anaerobic (does not require oxygen) not require oxygen)
- Splits 1 glucose molecule to 2 pyruvate molecules
- Requires input of 2 ATP molecules
- Generates 4 ATP molecules and 2 NADHmolecules
- In the presence of oxygen, pyruvate is then oxidized to form Acetyl CoA, entering the Citric acid
cycle
- The pathway of glycolysis consists of ten steps, each catalyzed by a specific enzyme. We can
divide these ten steps into two phases: The energy investment phase includes the first five steps,
and the energy payoff phase includes the next five steps.
- During the energy investment phase, the cell actually spends ATP to phosphorylate the fuel
molecules and NAD+ is reduced to NADH by oxidation of the food
Overall: 1 Glucose  2 Pyruvate + 2 ATP + 2 NADH