catalyses and the use of energy by cells

1. Catalysis & the use of energy
by cells
Mahnoor
Kifayat Ullah
Zohaib Hussain
Kiyanat Fiaz

2. •Living things create and maintain order
•Cells must perform stream of chemical reactions
•Cell is a tiny chemical factory
•Metabolism is an emergent property of life that arises
from specific interactions between molecules within
the orderly environment of the cell.
•Small molecules are assembled into polymers, which
may later be hydrolyzed as the needs of cell change.
2

3. Two Laws of Thermodynamics
• According to the first law of thermodynamics, the
energy of universe is constant.
• Energy can be transferred and transformed, but it
cannot be created or destroyed.
• This is also known as conservation energy.
3

4. The second law of thermodynamics
• Every energy transfer or transformation makes universe
more disordered.
• There is a quantitative measure of disorder, called
entropy, whose value increases as disorder increases.
• Therefore, second law of thermodynamics states that
every energy transfer or transformation makes universe
more disordered.
4

5. Where Do Cells Obtain Their Energy?
• Cells, like humans, cannot generate energy without
locating a source in their environment
• Sun is the ultimate source of energy for almost all cells
• Cellular nutrients come in many forms
• In order to provide a cell with energy, these molecules
have to pass across the cell membrane
5

6. How Do Cells Turn Nutrients into Usable Energy?
• Complex organic food molecules are rich sources of energy
for cells
• Bomb calorimeter
• Cells release the energy stored in their food molecules
through a series of oxidation reactions.
• Cells convert energy into small, energy-rich molecules such
as ATP and nicotinamide adenine dinucleotide (NADH)
6

7. How Do Cells Keep Energy in Reserve?
• Cells make larger, energy-rich molecules to store their
excess energy.
• Animal cells can also synthesize branched polymers
of glucose known as glycogen
• Plant cells make different glucose polymers known as
starches, which they store in granules.
7

8. Examples of energy storage within cells.
A) In this cross section of a rat kidney cell, the cytoplasm is filled with glycogen granules, shown here labeled with a black
dye, and spread throughout the cell (G), surrounding the nucleus (N). B) In this cross-section of a plant cell, starch
granules (st) are present inside a chloroplast, near the thylakoid membranes (striped pattern). C) In this amoeba, a single
celled organism, there is both starch storage compartments (S), lipid storage (L) inside the cell, near the nucleus (N)
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9. Cell Metabolism is organized by Enzymes
9

10. Cell Metabolism
• A cell's daily operations are accomplished through the
biochemical reactions
• Reactions are turned on and off or sped up and
slowed down according to the cell's needs
• Numerous pathways involved in building up and
breaking down cellular components must be
monitored and balanced in a coordinated fashion.
10

11. What Do Enzymes Do?
•Enzymes speed biochemical reactions by facilitating the
molecular rearrangements.
•Enzymes change shape when they bind with substrate
molecules.
•Enzymes function by bringing two substrates into close
proximity
•Shape or conformational changes can also act as an on/off
switch e.g. Inhibitor & Activator
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12. Enzymes are proteins that can change shape and therefore become active or inactive. An activator molecule
(green pentagon) can bind to an enzyme (light green puzzle shape) and change its overall shape. Note the
transformation of the triangular point on the green enzyme into a rounded shape. This transformation enables
the enzyme to better bind with its substrate (light pink puzzle piece). In contrast, an inhibitor molecule (pink
circle) can prevent the interaction of an enzyme with its substrate and render it inactive.
12

13. What Are Metabolic Pathways?
• Many of the molecular transformations that occur within
cells require multiple steps to accomplish.
• The coordinated series of chemical reactions form
metabolic pathway in which the product of one reaction
becomes the substrate for the next reaction.
13

14. How Do Cells Keep Chemical Reactions in Balance?
•Cells are expert recyclers
•Catabolic pathways & Anabolic pathways
•Cells must balance their catabolic and anabolic
pathways
•Example of glucose
14

15. Catabolic and anabolic pathways in cell metabolism
Catabolic pathways involve the breakdown of nutrient molecules (Food: A, B, C) into usable forms (building blocks). In this
process, energy is either stored in energy molecules for later use, or released as heat. Anabolic pathways then build new
molecules out of the products of catabolism, and these pathways typically use energy. The new molecules built via anabolic
pathways (macromolecules) are useful for building cell structures and maintaining the cell. 15

16. How Do Cells Manage All Their Chemical Reactions?
• Cells must monitor the needs and surpluses of all their
different metabolic pathways.
• Use of activators & inhibitors
• Up- and down-regulation of metabolic pathways is
often a response to changes in concentrations of key
metabolites
• Feedback inhibition
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17. Feedback inhibition
When there is enough
product at the end of a
reaction pathway (red
macromolecule), it can
inhibit its own synthesis by
interacting with enzymes in
the synthesis pathway (red
arrow).
17

18. References
Essentials of Cell Biology, Unit 1.3
Cell Biology for Seminars, Unit 1.3
Essentials of Cell Biology, Unit 1.5
Qian H. et al. (2011) doi:10.1371/journal.pone.0019451.
Letcher P. M. et al. (2013) doi:10.1371/journal.pone.0056232.
Bamri-Ezzine, S. et al. (2003) doi:10.1097/01.LAB.0000078687.21634.69.
18

19. Biological Order Is Made Possible By The
Release Of Heat Energy From Cell
KIFAYAT ULLAH
SP17-R02-003
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20. 20
The universal tendency of things to become disordered is a
fundamental law of physics the second law of thermodynamics
The level of disorder in the universe is steadily increasing.
Systems tend to move from ordered behaviour to more random
behaviour.
Examples:
• Heat flows from hotter to cold region.
• An ice cube melts in a glass of water.
• A glass falling off a table Shatter.

21. An everyday illustration of
the spontaneous drive toward disorder
21

22. How living cell generate order ?
• Living cell
• Survive
• Grow
• Forming complex organism.
• A cell is not an isolated system:
• It takes in energy from its environment in the form of
• Food
• Photons from sun
• Inorganic molecules.
• And it then uses this energy to generate order within itself.
22
Generate order ?
Ans

23. Figure: A simple thermodynamic analysis of a living cell
• The cell converts part of the energy it uses into heat.
• The heat is discharged into the cell's environment and disorders it,
• The 2nd law of thermodynamics is satisfied.
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24. Where does the heat that the cell releases
come from?
24

25. The first law of thermodynamics
• Energy can be converted from one
form to another, but that it cannot
be created or destroyed.
• For example, an animal cell takes
in foodstuffs
• Converts (chemical bond energy)
into the random thermal motion of
molecules (heat energy).
25

26. Photosynthetic Organisms Use Sunlight to
Synthesize Organic Molecule
Photosynthesis
Two stages
• Energy Storage: Stored as
chemical bond energy in
specialized Carrier
Molecules (ATP,NADPH)
• Carbon fixation: Sugars
are manufactured from
CO2 & H2O
light energy + CO2 + H2O sugars + 02 + heat
energy 26

27. Plant Sun
Carbon: Atm CO2
H2 & O2: water
N2: Ammonia
Nitrates and other elements: Soil
• Polysaccharide
• Proteins
• Nucleic acids,
• Lipids
Stored in PlantAnimal
• Sugars,
• Amino acids,
• Nucleotides,
• Fatty acids
27

28. Cells Obtain Energy by the Oxidation of Organic
Molecule
• Cellular nutrients come in many forms, including
sugars and fats.
• In order to provide a cell with energy, these
molecules have to pass across the cell membrane
• Which functions as a barrier
• Semi permeable
• They may require some energy input to
accomplish this task.
28

29. How Do Cells Turn Nutrients into Usable Energy?
• Complex organic food molecules such as sugars, fats, and proteins are rich
sources of energy
• Stored within the chemical bonds that hold them together
• Cells release the energy stored in their food molecules through a series of
oxidation reactions in Cellular respiration.
C6H12O6 + 6O2 6 CO2+ 6 H2O + Energy (Heat or ATP)
29

30. Schematic representation of the controlled stepwise
oxidation of sugar in a cell, compared with ordinary
burning
Stepwise oxidation of sugar in a cell, Direct burning of sugar in non living system
30

31. • Cells do not use the energy from oxidation reactions as soon as it is released.
• They convert it into small, energy-rich molecules
• ATP and
• NADH (Nicotinamide adeninedinucleotide )
• Which can be used throughout the cell to power metabolism and construct new
cellular components.
• Enzymes use this chemical energy to catalyze, or accelerate, chemical reactions
within the cell that would otherwise proceed very slowly.
31

32. The Living World9th Edition
By George Johnson
Copyright: 2018
Unit 2 chap 7
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33. Photosynthesis and respiration are complementary processes
http://mcdowellplants.weebly.com/
uploads/2/1/2/4/21242264/7796140_
orig.png 33

34. Kiyanat Fiaz

35. ATP IS THE MOST WIDELY USED ACTIVATED
CARRIER MOLECULE
• A critically important macromolecule—arguably “second in
importance only to DNA”—is ATP
• ATP is a complex nanomachine that serves as the primary energy
currency of the cell,
• ATP is the “most widely distributed high-energy compound within
the human body”
• This ubiquitous molecule is “used to build complex molecules,
contract muscles, generate electricity in nerves,.
35

36. CONT.
• Energy is usually liberated from the ATP molecule to do work in the
cell by a reaction that removes one of the phosphate-oxygen groups,
leaving adenosine diphosphate (ADP).
• When the ATP converts to ADP, the ATP is said to be spent. Then the
ADP is usually immediately recycled in the mitochondria where it is
recharged and comes out again as ATP.
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37. ENERGY STORED IN ATP IS OFTEN HARNESSED
TO JOIN 2 MOLECULES
• An energetically favorable reaction can be coupled to an energetically
unfavorable reaction, X → Y, so as to enable it to occur.
• In that scheme a second enzyme catalyzes the energetically favorable
reaction Y → Z, pulling all of the X to Y in the process.
37

38. 38

39. CONT.
• A frequent type of reaction that is needed for biosynthesis is one in which
two molecules, A and B, are joined together to produce A-B in the
energetically unfavorable condensation reaction.
• Energy from ATP hydrolysis is first used to convert B-OH to a higher-energy
intermediate compound, which then reacts directly with A-H to give A-B.
The simplest possible mechanism involves the transfer of a phosphate from
ATP to B-OH to make B-OPO3, in which case the reaction pathway contains
only two steps:
39

40. CONT.
• B-OH +ATP->B- O+PO3 +ADP
• A-H + B-O-PO3A-B +Pi
40

41. 41

42. 42

43. Oxidation & Reduction
involves electron transfer
43

44. Organic material
Burn
Single Step
Heat
Direct addition of oxygen
Metabolism
Multiple Steps
Enzymes
No direct addition of
oxygen
Cellular process Vs Burning

45. Oxidation - Reduction
• Oxidation is loss of electrons
• Reduction is gain of electrons
• Oxidation is always accompanied by reduction
• The total number of electrons is kept constant
• Oxidizing agents oxidize and are themselves reduced
• Reducing agents reduce and are themselves oxidized
45

46. Follow the Electrons
46

47. Combustion of Sugar (or respiration).
• The number of electrons is conserved
• Oxidation and reduction always occurs simultaneously
• Glucose reacts with molecular oxygen to produce carbon dioxide
and water.
• The carbon atoms in glucose are oxidized. That is, they lose electron
and go to a higher oxidation state.
• The oxygen atoms in molecular oxygen are reduced. That is, they
add electrons and go to a lower oxidation state
47

48. Reaction
48

49. Formation of Polar Covalent Bond
49

50. Hydrogenation & Dehydrogenation
Increase C-H Bonds
(Hydrogenation/Reduction)
Decrease C-H Bonds (Dehydrogenation/Oxidation)
50

51. How enzymes find their
substrate: the enormous
rapidity of molecular
motions
51

52. How do E & S find each other?
• Enzyme Substrate reaction rate = (1000 substrate molecules/ Seconds )
• Thus Enzyme bind to substrate for a milliseconds
• High Molecular level motions due to heat energy
• Translational motion
• Vibration
• Rotations
Meaured by spectroscopic techniques
52

53. Diffusion
Molecules are also in constant translational motion, which causes them
to explore the space inside the cell very efficiently by wandering
through it-a process called diffusion.
53

54. Random Walk
Every molecule in a cell collides with a huge number of other molecules
each second. As the molecules in a liquid collide and bounce off one
another, an individual molecule moves first one way and then another,
its path constituting a random walk
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55. • Average net distance that each molecule travels (as the crow flies)
from its starting point is proportional to the square root of the time
• 1second to travel 1 µm
• 4 seconds to travel 2 µm
• 100 seconds to travel 10 µm
• A small organic molecule, for example, takes only about one-fifth of a
second on average to diffuse a distance of 10 pm
Random Walk
55

56. Rate of Encounter
• The rate of encounter of each enzyme molecule with its substrate will
depend on the concentration of the substrate molecule.
• Abundant substrates = Concentration of 0.5 mM.
• Pure water is 55.5 M,
• One such substrate molecule in the cell for every 10s water
molecules.
56

57. • Active site on an enzyme molecule that binds this substrate will be
bombarded by about 500,000 random collisions with the substrate
molecule per second.
57
Rate of Encounter

58. 58
Stronger the binding of the enzyme & substrate, the
slower their rate of dissociation.

59. Once an enzyme and substrate have collided and
smuggled together properly at the active site, they form
multiple weak bonds with each other that persist until
random thermal motion causes the molecules to
dissociate again
59
Weak Binding

60. Two colliding molecule poorly matching surfaces Few non-
covalent bonds and their total energy is negligible compared
with that of thermal motion. Two molecules dissociate as
rapidly as they come together, preventing incorrect Link
between an enzyme and the wrong substrate
60
Strong Binding

61. 61