3 - Biochemical processes in cells

1. ENERGY

2. Organisms obtain their energy by breaking down
complex high-energy biomolecules
(otherwise known as food)
AUTOTROPH
Can utilize sunlight as an
energy source
Plants and photosynthetic
bacteria & protists
HETEROTROPH
Must consume organic matter
to obtain energy (in the form of
chemical energy)
Animals, fungi and non-
photosynthetic bacteria &
protists

3. Energy
High energy compounds (ie carbohydrates,
fats and alcohols) are broken down to low
energy compound (ie water, carbon dioxide
and oxygen)
Chemical reactions in the body can be
exergonic (release energy) aka catabolic
Chemical reactions in the body can be
endergonic (require energy) aka anabolic
Often exergonic and endergonic reactions in
the body will be complimentary

4. Exergonic and Endergonic Reactions

5. Example of complimentary exergonic
and endergonic reactions

6. Example of
complimentary
exergonic and
endergonic
reactions

7. ENZYMES

8. Enzyme Structure
Some are pure proteins
Some require COFACTORS to work (usually
inorganic metal ions)
Eg. iron, copper, calcium, zinc, potassium
Some require COENZYMES to work (an
organic substance)
Eg. a vitamin

9. Enzyme Structure
Enzymes have an active site and a regulatory region
The active site (formed by folds in the protein) is where
substrate binds to the enzyme
The regulatory region is where cofactors coenzymes or enzyme
inhibitors can alter the function of an enzyme
Substrate
Active site
Regulatory region
Products
Enzyme inhibitor

10. Some quick facts.
Enzymes …
Act at both the intra and extracellular level
Act on SUBSTRATE and yield PRODUCT
Reduce the ACTIVATION energy required to
start a reaction in the body
Are very specific, each individual type of substrate is acted upon by a specific enzyme

11. The “Lock and Key” model of enzyme
activity
The enzyme provides a perfect fit for a
particular substrate

12. The “Induced Fit” model of enzyme
activity
The substrate induces the enzyme to change
shape to create a tighter fit

13. Factors Affecting Enzyme Activity
pH
Most biological enzymes operate
at a neutral pH range of 6-8
If enzymes are at a pH outside
their optimum range, their shape
will change and they will be less
efficient.
2.08.07.47.6Opt. pH
StomachSmall
Intestine
Blood
Cells
Location
PepsinTrypsinCarbonic
Anhydrase
Enzyme

14. Factors Affecting Enzyme Activity
Temperature
Most biological enzymes have an optimum
temperature of 37°
If an enzyme is exposed to temperatures higher than
optimum, it will permanently denature.
If an enzyme is exposed to temperatures lower than
optimum, it will become inactive until temperature
returns to optimum.
The enzymes of other organisms have optimum
temperatures suited to the environment in which they
live

15. Factors Affecting Enzyme Activity
Enzyme Concentration
An increase in enzyme conc. will cause an
increase in reaction rate but won’t increase
the yield.
Substrate concentration
Reaction rate will initially increase as unoccupied enzymes take on substrate but will then plateau.
Inhibition
Other molecules can block the active site or regulatory region of an enzyme.

16. Increasing substrate concentration

17. PhotosynthesisPhotosynthesis

18. Photosynthesis
The process in which light energy is
transformed in to chemical energy
Performed by
Plants
Algae
Some protists (eg phytoplankton)
Photosynthetic bacteria

19. What makes leaves so ideal for
photosynthesis?
Flat = large surface area to volume ratio
Many stomata = efficient import of CO
2
and
export of O
2
Thin with many air chambers = diffusion of
CO
2
Xylem = transports reactants in
Phloem = transports products out
Chloroplasts = photosynthetic pigment
concentrated in dedicated organelles

20. Chloroplasts

21. The Photosynthetic Equation
Photo = light
Synthesis = put together
It is a complex series of reactions that can be
summarized as:
12H
2O + 6CO
2 → 6O
2 + C
6H
12O
6 + 6H
2O
6 of the water molecules on either side of the
equation cancel each other out to give:
6H
2O + 6CO
2 → 6O
2 + C
6H
12O
6

23. Photosynthesis OverviewPhotosynthesis Overview
6H
2
O + 6 CO
2
--> C
6
H
12
O
6
+ 6 O
2
Light Dependent Stage
H
2
O --> O
2
requires Light E
Light Independent Stage
CO
2
--> 2x3C sugars

24. Light-dependent reaction
Inputs: sunlight, water, NADP, ADP & P
i
Outputs: oxygen, ATP & NADPH
A not-so-simple explanation
of the process

25. A simplified version of the process

26. Light-dependent reaction
Occurs in the grana
Light energy is used to split water in to two H
+

ions and O
2
gas
The O
2
is released as waste
With the power of the two free electrons
One H
+
ion fuses ADP to P
i
to form ATP
One H
+
ion fuses to NADP to form NADPH

27. Inputs Outputs
Water H
2
O ATP
Electron e
-
NADPH
NADP
+
ADP + P
Oxygen (“waste”)

28. Light-independent stageLight-independent stage
Occurs in Stroma
Does not need light, but NADPH and ATP
from previous stage
Needs CO
2
and H
+
ions
Sugar molecules are synthesised from CO
2
CO
2
= oxidised state (low E compound)
C(H
2
O)n = reduced state (high E compound)
NADPH (carrier H
+
) is the reducing agent
ATP is the energy source

29. Inputs Outputs
ATP ADP + P
NADPH NADP
+
3C -> Glucose

30. Carbon reduction in Carbon reduction in CC
33 Plants Plants
Calvin Cycle
Called C
3

plants as the
end product is
a 3-carbon
compound
(PGAL), that
goes on to form
glucose.
Photosynthesis
occurs in the
mesophyll cells,

31. Carbon reduction in CCarbon reduction in C
44 plants plants
Plants in hot, dry habitats and important crop
plants such as corn, sugar cane
If light independent reaction took place in
mesophyll cells, these plants would lose too
much water from their open stomata.
One step occurs (in the mesophyll cells) to
transport CO
2
(in the form of oxaloacetate) to
the bundle sheath cells,

32. Carbon reduction in CCarbon reduction in C
44 plants plants
CO
2
combines with the 3-
carbon compound PEP
(phophoenolpyruvic acid) to
form oxaloacetate (4C)
A further reaction converts
oxaloacetate (4C) to malate
(4C).
Then a CO
2 molecule leaves
the cycle to nter the Calvin
cycle, whilst the remaining 3C
pyruvate returns to reform
PEP.

33. C
3
PLANTS C
4
PLANTS

34. Putting Photosynthesis togetherPutting Photosynthesis together
2 x PGAL = fructose
fructose = glucose
fructose + glucose = sucrose
glucose x
∞
= starch

36. General Info on Cellular
Respiration
Organisms can’t use glucose (2800 kJ) as
energy, needs to be broken down to approx
1/100
th
of its size – ATP (30 kJ).
Breakdown is not 100% efficient (usually
36-38 ATP produced)
Remainder is lost as heat. Endothermic
organisms trap this heat with layers of fat to
maintain body temperature.

37. General Info on Cellular
Respiration
The rate of respiration depends on the state
of activity of the organism
Respiration involves 2 coupled reactions
Energy is released by the breakdown of
glucose
Energy is required for the production of ATP
There are 2 types of respiration
Aerobic respiration (requires oxygen)
Anaerobic respiration (does not require
oxygen)

38. Aerobic vs Anaerobic
Respiration

39. Aerobic respiration
C
6
H
12
O
6
+ O
2
→ CO
2
+ H
2
O
Outside cells, to oxidise glucose need temp
of 200° - Entire molecule oxidised
simultaneously
Inside cells, oxidised gradually in small steps
Steps summarized in to 3 stages
Glycolysis (produces pyruvate)
Krebs Cycle (2 required per molecule of
glucose)
Electron transport (harvests H
+
from carriers)

40. Glycolysis
Occurs in cytosol – uses
enzymes and vitamins as
coenzymes
1 glucose (6C) converted
to 2 pyruvate (3C)
Forms 2 ATP & 2 NADH
(from NAD – nicotamide
adenine dinucleotide)

41. Krebs Cycle
Occurs in mitochondria
Pyruvate initially broken down in to
CO
2
and Acetyl-coA
Joins with 4C molecule to form 6 C
molecule
CO
2
to form 5 C molecule, then again
to form 4 C molecule
Further oxidation takes place to
reform original 4C
Throughout cycle, constant oxidation
is fusing hydrogen to carrier
molecules NAD → NADH and FAD
→ FADH
2

42. Electron Transport
Occurs in inner membrane of
mitochondria
Produces 2-3 ATP per loaded receptor
Electrons passed from one
cytochrome to next until accepted by
O
2-
to form water
Return of released protons through
ATP synthase carrier provides energy
to produce ATP from ADP & P
i
(phosphorylation)

43. Summarising Aerobic Respiration
Vocabulary
Oxidation = removal of hydrogen
Reduction = addition of hydrogen
A total of 36 ATP are formed except in the cells of heart, liver and
kidneys where 38 are formed

46. Anaerobic respiration (in
humans)
Occurs in muscles where oxygen supply exceeds demand
The only stage that can occur is glycolysis
So 1 glucose produces 2 ATP
2 NADH convert pyruvate to lactate (lactic acid)
Lactate build up causes pH to fall and pain & muscle fatigue
When activity returns to normal and oxygen becomes available,
lactate converted back to pyruvate to enter the Krebs Cycle.

47. Anaerobic respiration (in yeast)
Anaerobic respiration in yeast is called
fermentation
Pyruvate is broken down in to CO
2
and
ethanol (alcohol)

48. What happens during starvation?
- Autophagia (feeding of self)