The document provides an overview of nitrogen metabolism. It discusses (1) the importance of nitrogen in proteins and nucleic acids, (2) the key anabolic processes of nitrogen fixation, amino acid synthesis and protein synthesis, and (3) the main catabolic processes of proteolysis, nitrification and denitrification. Nitrogen is obtained from the atmosphere through nitrogen fixation by bacteria and is used to synthesize amino acids and proteins essential for plant structure and function.
biological nitrogen fixation, which is carried out by diazotrophs, has been dealt with in this slideshare. it involves the mechanism involved and various factors involved therein.
Assimilation of ammonium ions is the ultimate aim of nitrogen metabolism in plants. this is the source of nitrogen for various organic compounds of structural and functional importance for the living world
it is bypass cycle of citric acid cycle.
it give the brief description of glyoxylate cycle.
it is the summary of glyoxylate cycle for m.sc, bsc, science students.
it is very important topic for entrance exam of biology stream.
nitrogen is the most abundant atmospheric gas,yet is a limiting factor. this presentation is a bird's eye view, of nitrogen cycle, its fixation, uptake and assimilation in plants
ATP synthase—also called FoF1 ATPase is the universal protein that terminates oxidative phosphorylation by synthesizing ATP from ADP and phosphate.
ATP Synthase is one of the most important enzymes found in the mitochondria of cells
this lesson explains the basic biochemical/biological process behind Nitrogen fixation by microorganism which could be symbiotic or non symbiotic/free living in mechanism.
nitrate and sulfate reduction ; methanogenesis and acetogenesisjyoti arora
this presentation includes following topics in brief:
1. nitrate assimilatory reduction
2. sulfate assimilatoery reduction
3. methanogenesis
4. acetogenesis
biological nitrogen fixation, which is carried out by diazotrophs, has been dealt with in this slideshare. it involves the mechanism involved and various factors involved therein.
Assimilation of ammonium ions is the ultimate aim of nitrogen metabolism in plants. this is the source of nitrogen for various organic compounds of structural and functional importance for the living world
it is bypass cycle of citric acid cycle.
it give the brief description of glyoxylate cycle.
it is the summary of glyoxylate cycle for m.sc, bsc, science students.
it is very important topic for entrance exam of biology stream.
nitrogen is the most abundant atmospheric gas,yet is a limiting factor. this presentation is a bird's eye view, of nitrogen cycle, its fixation, uptake and assimilation in plants
ATP synthase—also called FoF1 ATPase is the universal protein that terminates oxidative phosphorylation by synthesizing ATP from ADP and phosphate.
ATP Synthase is one of the most important enzymes found in the mitochondria of cells
this lesson explains the basic biochemical/biological process behind Nitrogen fixation by microorganism which could be symbiotic or non symbiotic/free living in mechanism.
nitrate and sulfate reduction ; methanogenesis and acetogenesisjyoti arora
this presentation includes following topics in brief:
1. nitrate assimilatory reduction
2. sulfate assimilatoery reduction
3. methanogenesis
4. acetogenesis
nitrate and sulfate reduction ; methanogenesis and acetogenesisjyoti arora
this powerpoint includes the following topics in brief:
1. Nitrate assimilatory reduction
2. Sulfate assimilatory reduction
3. Methanogenesis
4. Acetogenesis
. INTRODUCTION
Insecticides are chemicals specifically designed to kill or control insect populations. They are widely used in agriculture, public health, and other industries to protect crops, livestock, and human health from insect-related damage and diseases. Once applied, insecticides undergo various metabolic processes in insects, which can affect their effectiveness and potential environmental impact.
The metabolism of insecticides in insects involves several key mechanisms:
1. Absorption: Insecticides can enter an insect's body through various routes, such as ingestion, contact with the exoskeleton, or inhalation. The mode of entry depends on the formulation and application method of the insecticide.
2. Phase I metabolism: In this initial phase, insecticides are often transformed by enzymes into more polar compounds through processes such as oxidation, reduction, or hydrolysis. These metabolic reactions aim to make the insecticides more water-soluble and facilitate their elimination from the body.
3. Phase II metabolism: Once insecticides undergo phase I metabolism, they may be further conjugated with endogenous compounds such as sugars, amino acids, or glutathione. Conjugation reactions increase the water solubility of the insecticides even more, making them easier to excrete from the insect's body.
4. Detoxification mechanisms: Insects have developed various enzymatic systems to break down insecticides and render them less toxic. For example, insects possess enzymes like cytochrome P450 monooxygenases, esterases, and glutathione-S-transferases, which are involved in the detoxification of many insecticides. These enzymes can modify the chemical structure of insecticides, making them less harmful to the insect.
5. Excretion: Once metabolized, insecticides and their metabolites are eliminated from the insect's body. This process generally occurs through excretory organs such as Malpighian tubules, which function similarly to the kidneys in vertebrates. Insecticides and their metabolites can be excreted in the faeces, urine, or through other excretory pathways.
Microsomal oxidation refers to a type of metabolic reaction that occurs in the microsomes, which are subcellular organelles found in cells. Microsomes contain various enzymes, including cytochrome P450 enzymes, responsible for catalyzing oxidative reactions in the body.
A. Cytochrome P450 enzymes are a family of enzymes involved in the metabolism of a wide range of endogenous and exogenous compounds, including pesticides, toxins, and foreign substances. These enzymes play a crucial role in the oxidation, reduction, and hydrolysis of various molecules, making them more water-soluble and easier to eliminate from the body.
B. Microsomal oxidation mediated by cytochrome P450 enzymes involves the addition of an oxygen atom to a substrate molecule, resulting in the oxidation of the substrate.
prepared by Centurion university of technology and management, B.Sc Agriculture 1st year 2nd sem students;
Ram prasad Behera(180804130026)
Gargeya Ku. Naik(180804130001).
Plants absorb nitrogen from the soil in the form of nitrate (NO3−) and ammonium (NH4+). In aerobic soils where nitrification can occur, nitrate is usually the predominant form of available nitrogen that is absorbed. However this is not always the case as ammonia can predominate in grasslands and in flooded, anaerobic soils like rice paddies.[4] Plant roots themselves can affect the abundance of various forms of nitrogen by changing the pH and secreting organic compounds or oxygen. This influences microbial activities like the inter-conversion of various nitrogen species, the release of ammonia from organic matter in the soil and the fixation of nitrogen by non-nodule-forming bacteria.
Ammonium ions are absorbed by the plant via ammonia transporters. Nitrate is taken up by several nitrate transporters that use a proton gradient to power the transport.Nitrogen is transported from the root to the shoot via the xylem in the form of nitrate, dissolved ammonia and amino acids. Usually (but not always most of the nitrate reduction is carried out in the shoots while the roots reduce only a small fraction of the absorbed nitrate to ammonia. Ammonia (both absorbed and synthesized) is incorporated into amino acids via the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway. While nearly all the ammonia in the root is usually incorporated into amino acids at the root itself, plants may transport significant amounts of ammonium ions in the xylem to be fixed in the shoots.This may help avoid the transport of organic compounds down to the roots just to carry the nitrogen back as amino acids.
Nitrate reduction is carried out in two steps. Nitrate is first reduced to nitrite (NO2−) in the cytosol by nitrate reductase using NADH or NADPH. Nitrite is then reduced to ammonia in the chloroplasts (plastids in roots) by a ferredoxin dependent nitrite reductase. In photosynthesizing tissues, it uses an isoform of ferredoxin (Fd1) that is reduced by PSI while in the root it uses a form of ferredoxin (Fd3) that has a less negative midpoint potential and can be reduced easily by NADPH. In non photosynthesizing tissues, NADPH is generated by glycolysis and the pentose phosphate pathway.
In the chloroplasts,glutamine synthetase incorporates this ammonia as the amide group of glutamine using glutamate as a substrate. Glutamate synthase (Fd-GOGAT and NADH-GOGAT) transfer the amide group onto a 2-oxoglutarate molecule producing two glutamates. Further transaminations are carried out make other amino acids (most commonly asparagine) from glutamine. While the enzyme glutamate dehydrogenase (GDH) does not play a direct role in the assimilation, it protects the mitochondrial functions during periods of high nitrogen metabolism and takes part in nitrogen remobilization.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Body fluids_tonicity_dehydration_hypovolemia_hypervolemia.pptx
Overview of nitrogen metabolism
1. OVERVIEW OF NITROGEN METABOLISM
BHUVANA A R AND Dr. KAYEEN VADAKKAN
DEPARTMENT OF BIOTECHNOLOGY
ST. MARY’S COLLEGE, THRISSUR
2. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
INTRODUCTION
The entire spectrum of living chemical reactions ,
occurring in living systems - METABOLISM
Metabolism is broadly classified into two :
CATABOLISM – degradative processes concerned
with the breakdown of complex molecules to
simpler ones with release of energy.
ANABOLISM – biosynthetic reactions involving in the
formation of complex molecules from simple
precursors.
3. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
NITROGEN METABOLISM
Polymeric nitrogen containing compounds
proteins and nucleic acids that define the major
attributes of organism such as function and
structure.
Operation and mechanism of metabolic pathways
is provided by proteins.
Genetic information is stored in nucleic acid
polymers.
Each of the monomer of these macromolecules
has an individual metabolic pathway.
4. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
PROCESSES OF NITROGEN METABOLISM
Nitrogen - most prevalent essential macro- elements
which regulates plant growth, especially in agricultural
systems.
Main source of nitrogen for the construction of
nitrogenous organic compounds is the atmosphere.
Plants require higher amounts of nitrogen as it is
important in their structure and metabolism.
But unfortunately ,most plants cannot utilize it in its
elementary form. So they have to depend on the soil
and they acquire nitrogen in inorganic form either as
ammonium compounds or as nitrate.
5. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
Nitrogen metabolism includes both anabolic and catabolic processes
Anabolic processes are:
(i) Nitrogen fixation
(ii) Amino acid synthesis
(iii) Protein synthesis
Catabolic processes are:
(i) proteolysis and amino acid destruction
(ii) de-nitrification
(iii) nitrification
6. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
1. NITROGEN FIXATION
Process by which inorganic molecular nitrogen (N2)
from the atmosphere is incorporated first into ammonia
and then into organic compounds that are useful to
organism.
N2 + 8H+ + 8e- + 16 ATP = 2NH3 + H2 + 16ADP + 16 Pi
STEPS:
Atmospheric nitrogen is reduced by the
addition of hydrogen atoms.
As a result the bonds between the two nitrogen
atoms (N2 N N) are broken down resulting
in the formation of ammonia.
Ammonia thus formed is used for the synthesis
of amino acids.
7. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
Biological nitrogen fixation is carried out by a highly conserved
complex of proteins –nitrogenase Complex
Electrons are transferred from pyruvate to dinitrogenase via
ferredoxin (or flavodoxin) and dinitrogenase reductase.
Dinitrogenase reductase reduces dinitrogenase one electron at a
time, with at least six electrons required to fix one molecule of N2.
An additional two electrons are used to reduce 2 H to H2 in a process
that obligatorily accompanies nitrogen fixation in anaerobes, making
a total of eight electrons required per N2 molecule.
Another important characteristic of the nitrogenase complex is an
extreme liability in the presence of oxygen.
8. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
2. NITRIFICATION
Nitrification is the biological oxidation of ammonia or ammonium to nitrite
followed by the oxidation of the nitrite to nitrate.
Reaction 1 :converts ammonia to the intermediate,
hydroxylamine, and is catalyzed by the enzyme ammonia
monooxygenase.
Reaction 2 :converts hydroxylamine to nitrite and is catalyzed
by the enyzmer hydroxylamine oxidoreductase.
The first step is the oxidation of ammonia to nitrite
9. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
The second step in nitrification is the oxidation of nitrite (NO2-) to nitrate
(NO3-)
3. DENITRIFICATION
Denitrification is the process that converts nitrate to nitrogen gas.
Reaction 1 : represents the steps of reducing nitrate to dinitrogen
gas.
Reaction 2 represents the complete redox reaction of
denitrification.
10. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
ii) AMINOACID SYNTHESIS
Ammonia thus formed as a result of nitrogen fixation is not given out .It is
highly toxic and used for the synthesis of amino acids.
Amino acids are the building blocks for the synthesis of proteins.
The amino acids are transported through phloem to other parts of the plant
for the synthesis of proteins.
Majority of amino acids are synthesized in plants by two main processes :
1. Reductive animation :- In this process, ammonia reacts with α - ketoglutaric
acid to form glutamic acid in the presence of enzyme glutamate dehydrogenase.
A reduced coenzyme NADPH in leaves , NADH in roots is required.
α-Ketoglutarate + NH4 + NADPH ͢ L -glutamate + NADP + H2O
11. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
2. Transamination
Reversible reaction in which an alpha-amino group (-NH2) is enzymatically
transferred from an amino acid1 to an alpha-keto acid2 resulting in formation
of a new amino acid2 and another alpha-keto acid1 (derived from original
amino acid1)
This pathway is responsible for the deamination of most amino acids.
One of the major degradation pathways which convert essential amino acids to
nonessential amino acids.
12. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
Eg:
iii) PROTEIN SYNTHESIS
Proteins are made up of long chains of amino acids.
form of one or more chain called polypeptide chains.
Amino acids bond to each other by peptide or amide bonds.
13. OVERVIEW OF NITROGEN METABOLISM, BHUVANA A R, ST.MARY’S COLLEGE - THRISSUR
The carboxyl group (-COOH) of one amino acid reacts with the amino
group (-NH2)of the next amino acid ,releasing a molecule of water and
as a result peptide bond (-CONH_) is formed.
This maybe illustrated with the two simplest amino acids, glycine and
alanine:-