Biology 233

Biology for engineer

 Chapter 5

Rules of metabolism
 General concept of energy in life

Thermodynamics concept: (Laws of thermodynamic)

First law: Energy (E) is not created or destroyed; it converted from

one form to another.
Second law: Entropy tends to increase.
Entropy: it measures how much energy in the universe
is dispersed or the increase of disorder

If entropy increases in one place it decreases in another place.

Energy is required to reduce entropy

Energy: is in play (been utilized) or stored. Energy flows through out life
by making and breaking bonds in chemical reactions.
 Energy in, Energy out
All chemical bonds holds potential energy .
Energy measured in Calories
Calorie: amount of energy required to heat one g of water by one degree at standard
pressure .

Reactants : molecules enter the reaction

Products : molecules that are formed following the reaction
Endergonic : Reaction that require input of energy (endothermic )
Exogonic : Reaction that release energy (exothermic)
Energy tend to flow in one direction,
and toward maximum dispersal.

Sun-------Producer ---------Consumer
ATP in Metabolism
ATP= Adenosine triphosphate ( a nucleotide found in DNA or RNA)
ADP= Adenosine diphosphate

In biology:
a. Energy is stored in ATP molecules

b. Energy is stored by conversion of ADP to ATP

is released by conversion of ATP to ADP
Energy

ADP + P ATP (storage of Energy)

Energy
Adenine
(purine) Ribose
(sugar)
Energy from the
sun or from food

Energy release
2 Phosphates
 Diffusion and Gradients (Chapt 5.6)

Diffusion= The net movement of molecules down their concentration

gradients (from high to low concentrations)

Mechanism of diffusion
* molecules are always in motion
* they collide at random and are kicked out (millions of time per
second)
* more are kicked out if concentration is higher
*thus will be diluted where concentration is lower
 time

Each molecule changed position

Movement of molecules By chance (probability),

=collision (more than 106/second)
each molecule would be at any given
= molecules changed position
position
If different molecules

time

red molecules will occupy any position

Diffusion: net movement of molecules down to a concentration gradient

(from higher concentration to lower concentration)
A substance diffuses in a direction set by its own concentration gradient, not by the
gradients of other solutes around it
Examples of Diffusion
 The Rate of Diffusion

Rate of diffusion depends on five factors:

– Size of molecules (smallest mover faster=higher rate)
– Temperature (higher temperature= higher rate)
– Steepness of the concentration gradient (higher gradient=
higher rate)
– Charge (positive/negative) [ will depend upon ions]
– Pressure [high difference pressure= higher rate]
 How substances cross membranes

Membrane: controls molecules in and out by selective permeability

• Gases and small non-polar molecules: diffuse freely across the

membrane (normal diffusion)

• Ions and large polar molecules:

require other mechanisms to cross the cell
membrane
* Passive transport (no energy expenditure)
* Active transport (requires energy
expenditure)
* Endocytosis and exocytosis (bulk
movements)
 Diffusion and Passive Transport
Diffusion
* Gases and small non-polar molecules

Passive transport (facilitated diffusion)

* Requires no energy input
* A specific protein allows the solute to follow its concentration
gradient across a membrane
 Active Transport

Active transport:
* Requires energy input (usually from ATP)
* Moves a solute against its concentration gradient, to the
concentrated side of the membrane

Example: Calcium pumps

– Active transporters move calcium ions across muscle cell
membranes
Active Transport: Example Calcium Pump
Active transport:
Example 2:
Cotransport: Sodium-Potassium Pump
 Which way will water move
• Osmosis: The movement of water down its (own)
concentration gradient – through a selectively permeable
membrane from a region of lower solute concentration to a
region of higher solute concentration

• Tonicity
– The relative concentrations of solutes in two fluids
separated by a selectively permeable membrane
 Mechanisms of tonicity

For two fluids separated by a semi-permeable membrane:

** Hypotonic= fluid with lower solute concentration
** Hypertonic= fluid with higher solute concentration

** Isotonic= fluids with the same solute concentration

Water: diffuses from hypotonic to hypertonic

: balances the concentrations of solute in
the 2 fluids
Osmosis
Tonicity
Tonicity of human cells, fluid,
plasma
= 0,9% NaCl
 Effects of Fluid Pressure in Plants

• Hydrostatic pressure (turgor)

– The pressure exerted by a volume of fluid against a
surrounding structure (membrane, tube, or cell wall)
which resists volume change; ex. plants

• Osmotic pressure
– The amount of hydrostatic pressure that can stop water
from diffusing into cytoplasmic fluid or other hypertonic
solutions;
Turgor= water pressure on the cell (in plant, in big vacuole)

pressure for water into the cytoplasm

Water

If Turgor increases

Turgor is high enough to prevent water to get

into cytoplasm= osmotic pressure
 How substances cross membranes

Membrane: controls molecules in and out by selective permeability

• Gases and small non-polar molecules: diffuse freely across the

membrane (normal diffusion)

• Ions and large polar molecules:

require other mechanisms to cross the cell membrane
* Passive transport (no energy expenditure)
* Active transport (requires energy expenditure)
* Endocytosis and exocytosis (bulk movements)
 Exocytosis and Endocytosis

• Endocytosis (into the cell)

– The formation of a vesicle from cell membrane, enclosing
materials near the cell surface and bringing them into the
cell
• Exocytosis (out of the cell)
– The fusion of a vesicle with the cell membrane, releasing its
contents to the surroundings
 Three types of Endocytosis

• Bulk-phase endocytosis
– Extracellular fluid is captured in a vesicle and brought into
the cell

• Receptor-mediated endocytosis
– Specific molecules bind to surface receptors, which are
then enclosed in an endocytic vesicle

• Phagocytosis
– Pseudopods engulf target particle and merge as a vesicle,
which fuses with a lysosome in the cell
 Example of Phagocytosis

Cells that can carry out phagocytosis include: Amoeba, white blood cells..
 Animation: diffusion and Tonicity

http://www.youtube.com/watch?v=w3_8FSrqc-I
 Enzymes in metabolic reaction
• Enzymes = catalysts (in chemistry)
* make a specific reaction occurs much faster than it would
on its own
* are not consumed or changed by participating in a
reaction
* most are proteins, some are RNA

Substrate: * The specific reactant acted upon by an enzyme.

Active site :* Pocket in enzymes where substrates bind for

the reaction to proceed.
Activation energy (AE)
= minimum amount of energy required for a reaction to start

Glucose + O2 (air) CO2 + H2O + E (more than a century)

(Instantaneous)

Spark (E)
Activation Energy (AE) Transition state = state from which the
reaction proceeds spontaneously

Substrates
A+ B [Ex. Spark (small energy)]

Products
C+D

Enzyme: * reduces AE, making the reaction to happen

* takes the reaction to a transition state
 How the enzyme works ?
Transition state is reached by 4 mechanisms:
– Helping substrates get together (binding to active sites)

– Orientating substrates in positions that favor reaction

– Inducing a fit between enzyme and substrate (induced-fit model

– like “lock and key”)
* Enz. restrains a substrate to a particular shape
* Enz. forces the substrates to fit into the active site

– Shutting out water molecules

Enzyme reaction in active site
 Controls Over Metabolism

• Concentrations of reactants or products can make

reactions proceed forward or backward

• Feedback mechanisms can adjust enzyme

production, or activate or inhibit enzymes
 Controls Over Metabolism

• Concentrations of reactants or products can make

reactions proceed forward or backward

• Feedback mechanisms can adjust enzyme

production, or activate or inhibit enzymes

• Allosteric control: is the regulation of the enzyme

at a site different from the active site, either by
inhibition or activation
Allosteric Control
Allosteric activator Allosteric inhibitor
Feedback Inhibition – a switching
action
http://www.youtube.com/watch?v=Pvgpk75us18&feature=related
 Effects of Temperature, pH, and Salinity

Each enzyme has its own optimum range of:

* Temperature (To):
High To= high reaction rates but too high To denature enzymes
low To = low reaction
* pH:
In humans, most enzymes work between pH 6 to 8
* salt concentration:
Affect the hydrogen bonds that hold enzymes in their three-
dimensional shape
 Optimum
temperature
Enzyme activity

35o C > 38 oC
temperature
Hypothermia [fever], lowers
Low enzyme activity enzyme reactions
Effect of pH and salinity

* Same type of graphs as the temperature with optimum pH and salinity values
of the enzymes..

* In human, most enzyme pH are around blood pH (7-8),

However some enzymes have different pH
Example:
Pepsin (enzyme that breakdown protein in stomach, with an optimum
pH 1-2)

but enzyme such trypsin and chemotrypsin (breakdown proteins in the

intestines) are active at high pH 8)
 Enzymes and helpers
Cofactors= Enzyme helpers
* Atoms or molecules (other than proteins) that are
necessary for enzyme function
Type of cofactors:
1. Metal ion (Fe, Cu, Zn, ect..)
Catalase (has iron, Fe) : Antioxidant enzymes that reduces free
radicals (unpaired electron).
2. Coenzymes
* Are organic cofactors such as vitamins
* May become modified during a reaction
– Ex. NAD+, NADP+
 Types of Metabolic Pathways

* Metabolic pathway or metabolism = Any enzyme-mediated

reactions in the cell.
**Three types:
Anabolic pathways: build molecules.
Catabolic pathways : break apart molecules.
Cyclic pathways: regenerate a molecule from the first step.

* Classification of organisms according to source of Carbon:

1- Autotroph: Make their own food and use CO2 as source of C:
(sun + CO2)
2- Heterotroph: Use organic molecules from autotroph as food and
source of C
Solving problem using Biology and engineering..

Water Purification:

Osmosis
Reverse Osmosis

Ind
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tri
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pp
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tio
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External pressure
 The largest reverse osmosis desalination plant in Saudi Arabia, Red Sea, 150Km from Jeddah

Abengoa awarded the construction of the largest reverse osmosis desalination

plant in Saudi Arabia

capacity of 600,000 m3/day, largest desalination plant using reverse osmosis

technology in Saudi Arabia.
 Application of diffusion and osmosis: dialysis

• Filtering of blood as the result of kidney failure

• Use of a filtering membrane that select based on the size (dialysis bag). Toxic molecules mainly urea are of small size,
therefore and is let to pass, but big molecules and cells do not pass and remained in the blood.

• Explain or draw how such blood filtering system

• Discuss the main problem associated with this system, and

propose some solutions
Application of diffusion and osmosis
Home assignment:

Give 5 different names of enzymes and their role in cell biochemistry