Saturday, August 20, 2016

The Protein Folding Problem: Anfinsen hypothesis and Levinthal paradox

Dr. Aditya Arya, Dr. Amit Kumar
Date of publication: 21 Aug 2016

We all know that proteins fold spontaneously on keeping them in suitable aqueous environment. However, there are some deeper questions which we must know about protein folding that, what are the models of proteins folding? Which route does a protein follow while folding? And how protein folding does not defy the second law of thermodynamics despite of the fact the randomness of protein itself is reduced on folding? We would also understand two famous hypothesis put forth by Levinthal and Anfinsen and various probability based question arising about the protein structure. . Infact the work of Anfinsen was recognized globally and he was awarded Nobel Prize in chemistry in the year 1972. Finally this note will end with a few practice MCQs based on the two key concepts.
There have been a number of questions in MSc entrances including JNU, IISc and TIFR on anfinsen hypothesis and levinthal paradox. 




Sunday, July 24, 2016

Illustrated Summary of Metabolism 
Dr. Aditya Arya
Date of publication: 24.07.2016


Metabolic processes are so complicated and it is difficult to understand them especially when we observe the individualistic approach. In biochemistry, It is equally important to have a bird eye's view on overall metabolism of various bio molecules to get a clear idea of what is happening to food that we eat. How it is digested, transported and utilised in the body. Liver is central to all metabolic processes and the functions of liver are regulated under the tight control of nervous system and hormonal system. Here in this post I present you an illustrated view of the overall process. This is a PDF (non-printable) documents only intended for digital reading. These illustrations are closely related to classroom lectures, so students may also visit the you tube channel to view some of the related classroom lectures on Biochemistry to recall the content (click to visit channel)., This content is adopted from Concise Biochemistry - by Aditya Arya. Hope this will help in enhancing the understanding of the topic. 


Friday, July 8, 2016

Grassroots Academy official blog milestone.

Grassroots Academy thanks all its visitors for this milestone
We wish to serve you better......


Upcoming posts very soon

>>>> Polymerase Chain reaction
>>>> Analysis of Biochemistry and techniques questions of CSIR NET

Thursday, June 9, 2016

Proteolytic Enzyme: Basic information and cleavage rules

Dr. Aditya Arya
Date of publication: 10 June 2016

Cleavage pattern obtained from proteolytic enzymes are commonly used to determine the sequence of small proteins or peptides.  Most of the proteolytic enzymes are capable of cleaving the protein at specific positions. Cleaving a protein with specific enzyme and then analysing the fragments may help in the determination of the order of amino acids by simple logical reasoning.   In this quick note we will understand how to solve such questions and also a detailed view cleavage rules. Additionally, we will also understand the problem solving skills based on the cleavage rules. Concluding remarks include commercial applications of proteases. This note has been prepared by content provided by global experts in the field of proteins (European Molecular Biology Laboratory and Swiss Bioinformatics Institute).  


NOTE: Past years trends of CSIR-NET exam and other nationwide competitive exams have shown frequent usage of these rule in questions. The question might appear very difficult and cannot be solved if we do not know the cleavage rules.  Most of books and online solved papers have not provided any details or solutions of such questions and this is Exclusive content prepared by us. Hope this will help in your preparation. 


Sunday, June 5, 2016

LAST MINUTE ENZYMOLOGY PREPARATION for CSIR -NET ASPIRANTS

Understanding the fact that enzymology is one the key areas of many competitive exams and there is a lot of confusion over various type of regulation, we are providing you free access to one of the chapter (a few pages deleted) of our brand new "Concise Biochemistry" book which is further supported by a video lecture by author on the same topic. All the previously asked questions have been solved at the end of the chapter. 




Hope it will help in your last minute preparation. Good Luck.

CLICK here to download enzyme regulation chapter 

CLICK here to watch the video lecture on the same topic

Saturday, June 4, 2016

TIPS and TRICKS by Grassroots Academy

We hope that your preparation is going well, this is a new series of Tricks and Tips we are beginning with a small creative.. Hope You will like this.:   Best Wishes






Wednesday, May 25, 2016

Grassroots Academy Introduces "Concise Biochemistry" especially written for competitive exams including CSIR-NET

Dear Students, 

I am glad to present this book entitled “Concise Biochemistry” especially written for preparation of CSIR-NET/ICMR/GATE and many other nationwide competitive exams for MSc. courses. This book will also be useful as concise teaching guide, learning aid for university exams and as well as a general Biochemistry text.  Although students may opt for a large number of Biochemistry books (for CSIR-NET, GATE etc.) in the market written with the objective of preparing a support to these exams but they mostly provide MCQs and lack the conceptual knowledge that is needed to solve questions in these exams.  However, I should not include my critical evaluation for some of the finest books on biochemistry including Lehninzer Biochemistry by Nelson and Cox, Biochemistry by Voet and Voet and Harpers Biochemistry, Lippincott’s illustrated reviews,  which have been a source of inspiration and guidelines for me to write this book and I must acknowledge their authors for using their ideas and analogies at some instances in this book and  I would suggest students to read these books for any further details on the subject. As an additional advantage, this book is concise and focused for competitive exams distinguishing it from other books.
This book has been divided in the three parts, the first part is essential chemistry for biology that includes atomic structure, intermolecular interactions, bio-energetics and kinetics.  These topics are generally omitted or curtailed by many biochemistry books but as they are very important and frequently asked in exams. Student often find those topics difficult and waste time in searching good content on these topics especially in biological context. Second part of the book contains description on all the key biomolecules, some new information has also been added on all the biomolecules especially based on the trend of previous exams. The third part consist of Metabolism and its regulation by enzymes, Although metabolism is much curtailed, yet, I have included some important points in metabolism like tracing molecules and organ specific metabolism which will provide additional benefit to the student by reading these topics.
In order to make this book customized for exams, after each chapter one page concept map, solutions to previous year questions from that topic and some of the high yielding facts have been added. The purpose of these sections is to provide a memory aid to the students. Additionally an exam index and statistics of exam questions from various papers has also been provided in the beginning of each chapter.

Additionally you are being provided free access to a few curtailed videos of classroom lectures of Biochemistry on you tube   CLICK HERE 


With best Wishes for CSIR-NET Exam 

Dr. Aditya Arya, Grassroots Academy




DOWNLOAD SAMPLE PAGES of BOOK 

Wednesday, April 20, 2016

Flow cytometry: Principle and Applications
Dr. Aditya Arya, Dr. Amit Kumar

Date of publication: 22.04.2016

Flow cytometry is one of the most powerful technique for the research as well as clinical diagnosis that simultaneously measures and then analyzes multiple physical characteristics of single particles (often cells) by forcing them to flow in a fluid stream and analysing through a beam of light. The properties measured include a particle’s relative size, relative granularity or internal complexity and relative fluorescence intensity.  These characteristics are determined using  an orchestered optical and electronic system that records how the cell or particle scatters incident laser light and emits fluorescence.  This technology has applications in a number of fields, including molecular biology, pathology, immunology, plant biology and marine biology. It has broad application in medicine (especially in transplantation, hematology, tumor immunology and chemotherapy, prenatal diagnosis, genetics and sperm sorting for sex preselection). Also, it is extensively used in research for the detection of DNA damage, caspase cleavage and apoptosis. The articles will provide a basic information on principle and data representation in flow cytometry. 


Additionally, if you are interested in knowing the workflow of FACSCalibure (a signle laser flow cytometer from BD) you may like the following workflow (especially for researchers). 

Wednesday, April 13, 2016

An Introductory Note on Animal Developmental Biology for CSIR-NET Exam

CSIR-JRF-NET is undoubtedly one of the best exams you have in life sciences in India. It is often believed that it is one of the toughest exams due to the dynamic nature of the question pattern. But like the saying ‘’when the going gets tough, the tough gets going’’, and you are here for that.

In this post of mine and in the following posts, we will be looking into how to cope up with some of the interesting yet favourite topic of CSIR Life sciences exam- Developmental Biology. Yes, Developmental Biology is a subject which is not only very interesting (of course, as it talks about how we develop) but also a lot of questions are asked from this topic which are very easy to answer if one is thorough with this topic. So all you have to do is put in some of your efforts! 

What is developmental biology?

The study of how an egg becomes an adult organism: the process by which new members of a species are generated.

(Image Credit: Developmental Biology, 10th ed. Scott F. Gilbert)


Types of questions developmental biology seeks to answer

How do cells arising from a fertilized egg become different from one another? DIFFERENTIATION
How do cells become organized into complex structures such as limbs? PATTERNING and MORPHOGENESIS
What controls the behavior of individual cells such that these highly organized patterns emerge? PATTERNING and MORPHOGENESIS
How are the organizing principles of development embedded within the egg, and within the DNA? DIFFERENTIAL GENE EXPRESSION
How have changes in developmental program, and more specifically, changes in gene expression, led to the evolution of the great diversity of animal forms? EVO-DEVLOPMENT


Why study development?

Many disciplines can be applied and integrated into the field of development


Before starting with the topics of Developmental Biology, I am going to provide you a list of important topics from which questions are asked in CSIR most of the times

List of Important Topics

1) Gametogenesis
2) Interaction of Sperm and Egg cell in both Invertebrates and Vertebrates (Part C questions)
3) Capacitation and Prevention of Polyspermy: Fast Block and Slow Block (Part C questions)
4) Cleavage, Types of Cleavage in different types of eggs (Part B + C questions)
5) Cleavage in Sea Urchin + Fate Map, C. elegans + Axis Determination, Drosophila, Amphibians, Fishes, Birds and Mammals (Part B questions)
6) Gastrulation, Types of Movements in Gastrulation (Part C questions)
7) Gastrulation in Drosophila and Xenopus; Axis determination (Both are very important topics as many Part C as well as Part B questions are asked from this section)
8) Gastrulation in Mammals (Special emphasis to various developmental genes involved)
9) Vulva Development in C.elegans, Eye Lens Development, Limb Development (Part C questions)
10) Sex Determination in Drosophila (Part C question)
11) Metamorphosis and Regeneration 

Tuesday, April 12, 2016



Principles of Chromatography
Authors. Dr. Aditya Arya, Dr. Mohit Gupta and Mr. Rahul Raj
Date of publication: 12.04.16

Chromatography is an important biochemical technique that is used for the separation of mixtures, both for analytical and preparative purposes. Classification of Chromatography is one of the most confusing concept which is not illustrated well in many texts and infact internet search does not provide a better way of their classification. A thorough search of scientific literature was used to re-organize various types of Chromatography. Readers may have their own views of classifying but one thing that creates most of the confusion is, inclusion of Column chromatography is one of the sub-type (however, we should know that columns are used in many types of chromatography such as ion exchange, partition, GC, Affinity and many other types), so we should avoid using this as subtype. Also, there are numerous ways to categorise the chromatography. Such as based on the nature of solvent, state of solvent, purpose of chromatography and also most importantly the principle involved. Another important aspect that must be noted while comparing types of chromatography is that high performance chromtographies and advanced instruments should be excluded as those instruments may have more than one principles involved such as in normal HPLC machines one can use partition chromatography with normal phase or reverse phase. This note provides an illustrated classification of types of chromatography and their description. 

 

Sunday, March 27, 2016

Vitamins: Structure and Functions
Authors. Dr. Aditya Arya & Dr. Mohit Gupta
Date of publication: 27 March 2016

A nutrient that the body needs in small amounts to function and stay healthy. Sources of vitamins are plant and animal food products and dietary supplements. Some vitamins are made in the human body from food products. Vitamins are either fat-soluble (can dissolve in fats and oils) or water-soluble (can dissolve in water). Excess fat-soluble vitamins are stored in the body's fatty tissue, but excess water-soluble vitamins are removed in the urine. Examples are vitamin A, vitamin C, and vitamin E.  This quick note provides a detailed description of all types of vitamins with overview of classification, their nomenclature, structures, and dietary sources. The biological functions have been described with illustrations which will be useful for several exams. Direct questions on functions or structures have been asked frequently in many nationwide entrance exams for M.Sc. as well as research fellowship exams such as CSIR-NET, ICMR and ICAR etc.








Tuesday, February 23, 2016


List of Common Inhibitors (Rare collection)
Dr. Aditya Arya and Dr. Mohit Gupta
Date of publication: 23th Feb 2016


Inhibitors are frequently used in life science research to reveal many biochemical processes and molecule events. Although there are thousands of inhibitors available for research purpose, only few of them have become popular due to their association with landmark discoveries in biology (such as discovery of complete electron transport chain) or their clinical application (many antibiotics are potent inhibitors). Most often, the source of these inhibitors are biotic and thefore they have long history of usage even before their chemical nature and biological function were not identified. Here, We have compiled a small list of inhibitors (from various authentic sources), which may be very useful for preparation of exams, as they form some of the frequently asked questions. Also, this type of collection is rare in text book. 

Wednesday, January 27, 2016

SPECTROPHOTOMETRY
Aditya Arya*
Date of publication: 25th July 2015

Spectrophotometry is extensively used technique in biology and chemistry. This quick note provides an overview of principle, applications and some of the numerical problems recently asked in CSIR-NET examination.



Definition
Spectrometry is derived from the two words, one is ‘spectrum’ which means a scale of any parameter over a span of its extreme values  (if its light wavelengths – light spectrum, spectrum of m/z ratios – mass spectrum, or 2G spectrum – for radio frequencies)



Shannon entropy: A measure of scoring multiple sequence alignment  (GATE - BIOTECH - 16)
Aditya Arya*
Date of publication: 26th Jan 2016

Shannon entropy is a quantitative measure of uncertainty in a data set. In most instances it is possible to calculate the entropy scores for a multiple sequence alignment (MSA). Sequence alignments are primarily of two types a. pairwise alignment (used for comparison of pairs) and b. multiple sequence alignments (generally used for phylogenetic analysis). pairwise alignment is scored on the basis of classical scoring matrices, while Shannon entropy is a tool for scoring of multiple sequence alignment.

INTRODUCTION
Sequence variability within related protein sequences has long ago been recognized to show significant clues about their 3-dimensional structure and function. Wu and Kabat (1977) were the first to define a variability coefficient that led them to predict that segments of high amino acid variability in immunoglobulins correspond to their antigen binding sites. Thus, high variability regions in a group of related proteins are linked to the specificity of the molecules. On the other hand, regions with low variability are usually structural, or define regions of common function.

READ MORE

Thursday, January 21, 2016