Unit IIUnit IIMetal ions in Metal ions in

Biological systemsBiological systemsDr. SS. Vutukuru, Dr. SS. Vutukuru, M.Tech., Ph.D, PG DEMM.Tech., Ph.D, PG DEM

Nitrogen Fixation

Sources

• Lightning• Inorganic fertilizers• Nitrogen Fixation• Animal Residues• Crop residues• Organic fertilizers

Encyclopaedia Britannica, Encyclopaedia Britannica (1998)

Forms of Nitrogen• Urea CO(NH2)2• Ammonia NH3 (gaseous)

• Ammonium NH4

• Nitrate NO3

• Nitrite NO2

• Atmospheric Dinitrogen N2

• Organic N

Global Nitrogen Reservoirs

Nitrogen Reservoir

Metric tons nitrogen

Actively cycled

Atmosphere 3.9*1015 No

Ocean soluble salts

Biomass6.9*1011

5.2*108

YesYes

Land organic matter Biota

1.1*1011

2.5*1010

SlowYes

Roles of Nitrogen

• Plants and bacteria use nitrogen in the form of NH4

+ or NO3-

• It serves as an electron acceptor in anaerobic environment

• Nitrogen is often the most limiting nutrient in soil and water

Nitrogen is a key element for

• amino acids

• nucleic acids (purine, pyrimidine)

• cell wall components of bacteria (NAM)

Nitrogen Cycle

• Ammonification/mineralization• Immobilization• Nitrogen Fixation • Nitrification• Denitrification

Ammonification or Mineralization

R-NH2

NH4 NO2

NO3

NO2

NO

N2O

N2

Mineralization or Ammonification

• Decomposers: earthworms, termites, slugs, snails, bacteria, and fungi

• Uses extracellular enzymes initiate degradation of plant polymers

• Microorganisms uses:• Proteases,lysozymes,

nucleases to degrade nitrogen containing molecules

• Plants die or bacterial cells lyse release of organic nitrogen

• Organic nitrogen is converted to inorganic nitrogen (NH3)

• When pH<7.5, converted rapidly to NH4

• Example:

Urea NH3 + 2 CO2

Immobilization

• The opposite of mineralization• Happens when nitrogen is limiting in the

environment• Nitrogen limitation is governed by C/N

ratio• C/N typical for soil microbial biomass is 20• C/N < 20 Mineralization• C/N > 20 Immobilization

Nitrogen Fixation

• Energy intensive process :

• N2 + 8H+ + 8e- + 16 ATP = 2NH3 + H2 + 16ADP + 16 Pi

• Performed only by selected bacteria and actinomycetes

• Performed in nitrogen fixing crops (ex: soybeans)

Microorganisms fixing

• Azobacter• Beijerinckia• Azospirillum• Clostridium• Cyanobacteria

• Require the enzyme nitrogenase

• Inhibited by oxygen

• Inhibited by ammonia (end product)

Rates of Nitrogen Fixation

N2 fixing system Nitrogen Fixation (kg N/hect/year)

Rhizobium-legume 200-300

Cyanobacteria- moss

30-40

Rhizosphere associations

2-25

Free- living 1-2

Bacterial Fixation

• Occurs mostly in salt marshes• Is absent from low pH peat of

northern bogs• Cyanobacteria found in waterlogged

soils

Nitrification

Two step reactions that occur together :

• 1rst step catalyzed by Nitrosomonas2 NH4

+ + 3 O2 2 NO2- +2 H2O+ 4 H+

• 2nd step catalyzed by Nitrobacter

• 2 NO2- + O2 2 NO3

-

• Optimal pH is between 6.6-8.0

• If pH < 6.0 rate is slowed

• If pH < 4.5 reaction is inhibited

Denitrification

• Removes a limiting nutrient from the environment

• 4NO3- + C6H12O6 2N2 + 6 H20

• Inhibited by O2

• Not inhibited by ammonia• Microbial reaction• Nitrate is the terminal electron

acceptor

Metal ions

• Many metal ions have role in biological processes of the body

• The ions have different physical and chemical properties– Complex formation– Oxidation states

• Minerals in food

The most important ions

• Ion• Ca2+

• Mg2+

• Fe2+

• Cu2+

• Zn2+

• Co3+

• Na+

• K+

• Role:• 1.5-2% of body mass, bones, teeth• Bones and teeth, intracellular activity• Hemoglobin, O2 transfer• Cofactor in enzymes• Cofactor in enzymes,growth, healing• In vitamin B12• Water balance, nerve impulses, fluids

inside and outside cells

Oxygen transport proteinshemoglobin

Hemoglobin is a tetramer composed of two α and two β subunits

Each subunit contains an iron-porphyrin ring that binds oxygen

Oxygen binding is highly cooperative between each subunit

Oxygen transport

Hemoglobin as oxygen carrier

• In each hemoglobin molecule there are four heme groups

• Heme = Fe2+ surrounded by phorphyrin group, • As O2 carrier: O2 binds to Fe2+ as a ligand

• Reversible process

The transport of oxygen in blood- Haemoglobin

Oxygen Transport

• The resting body requires 250ml of O2 per minute.

• We have four to six billion haemoglobin containing red blood cells.

• The haemoglobin allows nearly 70 times more O2 than dissolved in plasma.

Hemoglobin

Binding of O2 alters the structure

Haemoglobin4 x Haem group + 4 x Polypeptide chain

Hemoglobin• Oxygen carrier protein• 4 subunits = 2 alpha + 2 beta• Normal adult = HbA = 22• Four heme groups - iron-

porphyrin compound at O2 binding site

• Iron containing porphyrin rings, only Fe2+ can bind O2

• Each heme combines with one globin protein chain

• Molecular weight of hemoglobin is 64,000

• Each gm of Hb can carry up to 1.31ml of O2, theoretically up to

1.39 ml/gm

Chemical Binding of Hemoglobin & Oxygen

• Hemoglobin combines reversibly with O2– Hemoglobin is the unoxygenated form– Oxyhemoglobin is when O2 combined

• Association and dissociation of Hb & O2 occurs within milliseconds– Critically fast reaction important for O2 exchange– Very loose coordination bonds between Fe2+ and O2,

easily reversible– Oxygen carried in molecular state (O2) not ionic O2-

Haemoglobin Saturation

• Haemoglobin saturation is the amount of oxygen bound by each molecule of haemoglobin

• Each molecule of haemoglobin can carry four molecules of O2.

• When oxygen binds to haemoglobin, it forms OXYHAEMOGLOBIN;

• Haemoglobin that is not bound to oxygen is referred to as DEOXYHAEMOGLOBIN.

Pathological Ligands of Hemoglobin• Ligands form covalent bonds to the ferrous iron in Hb • These bonds have more affinity to iron than oxygen which binds

weakly to Hb

• Carbon Monoxide– 250 times the affinity than oxygen– Does not dissociate readily– Requires hours to rid body of CO

• Nitric Oxide– Binds to Hb 200,000 times more strongly– Hemoglobin binds irreversibly to NO – Used to treat pulmonary hypertension

Hemoglobin & Myoglobin

• Myoglobin is single chained heme pigment found in skeletal muscle

• Myoglobin has an increased affinity for O2 (binds O2 at lower Po2)

• Mb stores O2 temporarily in muscle

Myoglobin and Hemoglobin

• Myoglobin– Increases O2 solubility in tissues

(muscle)

– Facilitates O2 diffusion

– Stores O2 in tissues

• Hemoglobin– Transports O2 from lungs to peripheral

tissues (erythrocytes)

Figure 7-17a

Sickle-cell

Capillary Blockage

Porphyrin

• Porphyrin rings are biological molecules used in a variety of essential chemical processes

•The two most well-known porphyrins are heme and chlorophyll

Because of their large conjugated double bond system, porphyrins typically absorb visible light

Chlorophyll’s green color, heme’s red, and the blue blood of some sea creatures are all a result of this absorbance

Additionally, the 4 nitrogen atoms at the center of the ring are excellent at conjugating metals because of their lone pairs

As a result, porphyrins are a common way to attach metals to proteins

Heme

Chlorophyll –porphyrins are important in plants, too!

Chlorophyll as a Photoreceptor

• Chlorophyll is the molecule that traps this 'most elusive of all powers' - and is called a photoreceptor. It is found in the chloroplasts of green plants, and is what makes green plants, green. The basic structure of a chlorophyll molecule is a porphyrin ring, coordinated to a central atom. This is very similar in structure to the heme group found in hemoglobin, except that in heme the central atom is iron, whereas in chlorophyll it is magnesium.

http://departments.colgate.edu/chemistry/images/geier-fig1.gif

Chrophyll

• Porphyrin is also part of the chlorophyll, the key substance for the photosynthesis of green plants, some algae and some bacteria.

• Chlorophyll absorbs mainly violet-blue and orange-red light and reflect green colour which give plants their green colour

• Several kinds of chlorophyll exist (chl a,chl b etc.). They differ from each other in details of their molecular structure and absorb slightly different wavelengths of light.

 

  Chlorophyll is composed of two parts; the first is a porphyrin ring with magnesium at its center, the second is a hyrophobic phytol tail.  The ring has many delocalized electrons that are shared between several of the C, N, and H atoms; these delocalized electrons are very important for the function of chlorophyll.  The tail is a 20 carbon chain stabilizes the molecule in the hydrophobic core of the thylakoid membrane.

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Photosynthesis Overview

• Two processes - each with multiple steps

– Light reactions • convert solar energy to chemical energy• light energy drives transfer of electrons to NADP+

forming NADPH• ATP generated by photophosphorylation• occur at the thylakoids

Photosynthesis Overview

• Two processes - each with multiple stages

– Calvin cycle • Named for Melvin Calvin who worked out many of the

steps in the 1940s• incorporates CO2 from the atmosphere into an organic

molecule (carbon fixation)• uses energy from the light reaction to reduce the new

carbon to a sugar• occurs in the stroma of the chloroplast

Interactions of light with chloroplast matter

• Light may be reflected, absorbed, or transmitted by matter

• Pigments such as chlorophyll absorb photons of different wavelengths (energy)

• Plants are green because red and blue light are absorbed and green light is transmitted and reflected

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Light

Chloroplast TransmittedLight

AbsorbedLight

ReflectedLight

Grana

Light is composed of particles called photons that act like waves. 

Visible light is also called photosynthetically available radiation (PAR) .

Changes in the wavelength of visible light (PAR) result in a change of color. 

Light with a wavelength of 450 nm is blue while light with a wavelength of 650 nm is red. 

COVERTING LIGHT ENERGY TO CHEMICAL ENERGY

1. The Chlorophylls and Carotenoids are grouped in Cluster of a Few Hundred Pigment Molecules in the Thylakoid Membranes. 2. Each Cluster of Pigment Molecules is referred to as a PHOTOSYSTEM.  There are Two Types of Photosystems known as PHOTOSYSTEM I AND PHOTOSYSTEM II. 3. Photosystem I and Photosystem II are similar in terms of pigments, but they have Different Roles in the Light reactions. 4. The Light Reactions BEGIN when Accessory Pigment molecules of BOTH Photosystems Absorb Light. 5. By Absorbing Light, those Molecules Acquire some of the Energy that was carried by the Light Waves. 6. In each Photosystem, the Acquired Energy is Passed to other Pigment Molecules until it reaches a Specific Pair of CHLOROPHYLL a Molecules. .

Photosystem

• Photosystem is composed of the Light Harvesting Complex (LHC) and the reaction center. The LHC is composed of hundreds of molecules of chlorophylls and accessory pigments.

• When any antenna molecule absorbs a photon, transferred to a particular chlorophyll a in the reaction center

• At the reaction center is a primary electron acceptor which removes an excited electron from the reaction center chlorophyll a

How a photosystem harvests light

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Reaction Center Closeup

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Chlorophyll a molecules

Primary electronacceptor

Absorption of light boosts energy of an electron.Energy is passedfrom molecule tomolecule in the light-harvesting complex until it reaches the reaction center

Reactioncenter

Two Types of Photosystems

• Photosystem I– reaction center chlorophyll a molecule– P700 - absorption peak at 700nm

• Photosystem II– reaction center chlorophyll a molecule– P680

Noncyclic Electron Flow

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PS II PS I

A mechanical analogy for the light reactions

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1) Photons of light boost energy of electrons.

2) Energy is extracted from electrons in the electron transport chain and used for ATP synthesis.

3) Another photon boosts energy of an electron which ultimately istransferred to NADPH

1)2)

3)

• No O2 generated• No NADH generated• Only ATP generated

Cyclic electron flow

cyclic photophosphorylation

P700

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Ferridoxin

Light (dependent)Reactions

• Happen ONLY in sunlight– Hence they depend

on light!

1. Light is absorbed by chlorophyll molecules

2. The energy generates molecules of ATP

Image from: Biology 11: College Preparation. Pg 74. Nelson, Toronto. 2003.

Summary

Image from: Biology 11: College Preparation. Pg 74. Nelson, Toronto. 2003.