how to get biochemichal information

8/13/2019 How to Get Biochemichal Information

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General ChemicalLiteratureHow To Get Biochemical Information

LOGO UNHAS

Created By :

Ripka Saputri (H31112286)

Darmawati (H31112285)

Annisa Nur Khaeruni ()

Et

CHEMISTRY DEPARTMENTSCIENCE FACULTY

HASANUDDIN UNIVERSITY2 13


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BAB I

INTRODUCTION

A. BACKGROUND

Biochemistry is the study of chemical processes in living organisms.

Biochemistry regulate all living organisms and life processes. By controlling

information flow through biochemical signaling and the flow of chemical energy

through metabolism, biochemical processes give rise to phenomena that seem magical

life. Over the last 40 years biochemistry has become so successful in explaining the

process of life that now almost all areas of the life sciences for the botanical drug

involved in biochemical research. The scope of biochemistry include the study of the

chemical composition of cells, the properties of compounds and chemical reactions that

occur in cells, the compounds that support the activities of living organisms and the

energy required or produced.

From Biochemistrys definition, we know that Biochemistry is one of complex

study and there are many sources about biochemistry like article, journal, sources in

internet. So HowTo Get Biochemical Information needed quickly ? so this paper

created to facilitate readers to get information needed quickly in the field of

biochemistry.

B. PROBLEM FORMULATION

Based on the above background, it can be a problem are:

1. How to find information about the biochemistry from primary sources (journals,

reports, dissertations, and thesis)

2. How to find information about the biochemistry from secondary sources (quotation,

textbooks, and magazines)

3.

How to find information about the biochemistry from the tertiary sources (Dictonaryand encyclopedia)

C. PURPOSE

The purpose of this paper is to learn how to obtain Biochemical information

needed quickly appropriately and focused situation. We hope the readers can understand

basic and techniques in literature search in the field of BioChemistry.


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BAB II

BODY (ISI)

Biochemistry, sometimes called biological chemistry, is the study of chemical

processes within and relating to, living organisms. Much of biochemistry deals with the

structures, functions and interactions of biological macromolecules, such as proteins,

nucleic acids, carbohydrates and lipids, which provide the structure of cells and perform

many of the functions associated with life. The chemistry of the cell also depends on the

reactions of smaller molecules and ions. These can be inorganic, for example water and

metal ions, or organic, for example the amino acids which are used to synthesize proteins.

The mechanisms by which cells harness energy from their environment via chemical

reactions are known as metabolism. The findings of biochemistry are applied primarily in

medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and

cures of disease. In nutrition, they study how to maintain health and study the effects of

nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to

discover ways to improve crop cultivation, crop storage and pest control.

In General Chemical Literature Course specially Biochemistry, there are many

literature sources like Journal, Report, Article etc. Those literature sources, divided to some

types like Primary sources which include Journal, report, Thesis ets. Secondary sources,

include textbook and Science magazine. And tertiary sources, include Dictionary and

encyclopedia.

A. PRIMARY SOURCES

Primary Sources is original sources which from the first place or the first person.

Include Journal, Report, Thesis, etc

1) Journal

A journal is an academic magazine published on a regular

schedule. It contains articles written by experts in a particular

field of study, based on research or analysis that the author, or

authors, did. That research might include case studies in the

medical field, primary source research in the field of history, or

literature analysis. Journal articles are written for experts or

students of that particular field who have an advanced field-

specific vocabulary and knowledge. For example, View Current Issue (Volume 154
http://jb.oxfordjournals.org/content/currenthttp://jb.oxfordjournals.org/content/current


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Issue 3 September 2013).The Journal of Biochemistry founded in 1922 publishes the

results of original research in the fields of Biochemistry,

2) Report

Report is a document containing information organized in a narrative, graphic, or

tabular form, prepared on ad hoc, periodic, recurring, regular, or as required basis.

Reports may refer to specific periods, events, occurrences, or subjects, and may be

communicated or presented in oral or written form. For example is report about

Recombinant DNA Technology: A students first practical application using the

Escherichia coli host, the pBluscript IISK+ cloning vector, and the bacteriophage

lambda insert. Who writes from Department of Biochemistry, University of Sydney,

Sydney, Australia

3) Thesis or Dissertation

A thesis or dissertation is a document submitted in support of candidature for

anacademic degree or professional qualification presenting the author'sresearch and

findings. In some countries/universities, the word "thesis" or a cognate is used as part of

abachelor's ormaster's course, while "dissertation" is normally applied to adoctorate,

while in others, the reverse is true.

The word dissertation can at times be used to describe atreatise without relation to

obtaining an academic degree. The term thesis is also used to refer to the general claim

of anessay or similar work.

B. SECONDARY SOURCES

Secondary sources is In contrast, a secondary source of information is one that was

created later by someone who did not experience first-hand or participate in the events

or conditions youre researching. Include Textbook and magazine

1) Textbook

A textbook or coursebook is a manual of instruction in any

branch of study. Textbooks are produced according to the

demands of educational institutions. Although most textbooks are

only published in printed format, many are now available as

online electronic books. For example is a book on titled

Biochemistry, 5th edition By Jeremy M Berg, John L Tymoczko,

and Lubert Stryer.

2) Science Magazine
http://jb.oxfordjournals.org/content/currenthttp://jb.oxfordjournals.org/content/currenthttp://en.wikipedia.org/wiki/Academic_degreehttp://en.wikipedia.org/wiki/Researchhttp://en.wikipedia.org/wiki/Bachelor%27s_degreehttp://en.wikipedia.org/wiki/Master%27s_degreehttp://en.wikipedia.org/wiki/Doctoratehttp://en.wikipedia.org/wiki/Treatisehttp://en.wikipedia.org/wiki/Essayhttp://en.wikipedia.org/wiki/E-bookhttp://en.wikipedia.org/wiki/E-bookhttp://en.wikipedia.org/wiki/Essayhttp://en.wikipedia.org/wiki/Treatisehttp://en.wikipedia.org/wiki/Doctoratehttp://en.wikipedia.org/wiki/Master%27s_degreehttp://en.wikipedia.org/wiki/Bachelor%27s_degreehttp://en.wikipedia.org/wiki/Researchhttp://en.wikipedia.org/wiki/Academic_degreehttp://jb.oxfordjournals.org/content/current


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A science magazine is a periodical publication with

news, opinions and reports about science for a non-expert

audience. A periodical publication for scientific experts, in

contrast, is called a "scientific journal". Science magazines

are read by non-scientists and scientists who want

accessible information on fields outside their specialization.

One of the most renowned magazines is the "Daily

Sciencia", made famous by its article on why fingers shrivel

when exposed to water for a substantial amount of time.

This shriveling allows for better grip under the water. 3) Science Meeting

a. Workshop and Seminary

Workshop is event where several people get together to solve a particular problem

and find solution. A workshop is a small scientific meeting. While the Seminar is

interpreted as a form academic instruction (discussion of scientific problems), both are

given in University, by a specific organization or given by professional. For example

the scientific seminar or workshop of Biochemistry is National Seminar of Science and

Science Education VIII with terms The Human and Nature Sustainab ility

Empowerment through Science, Mathematics and Education

b. Science Biochemical Society Conferences

The Biochemical Society offers an excellent wide-ranging programme of high-

quality scientific conferences, in the UK and abroad. Our events cover a wide spectrum

of topics; from stem cell technology to plant reproduction and from neuronal disease to

bionanotechnology. Proposals for conferences are welcome from any member of the

scientific community

13th International Conference on the Chemistry of Antibiotics and Other BioactiveCompounds that hold on 24 Sep 2013 27 Sep 2013 at Yamanashi, Japan

International Conferencefor Applied Sciences 'Current Queries in Biology,

Ecology, Medicine and Pharmacology' that hold on 26 Sep 2013 27 Sep 2013At

Dnepropetrovsk, Ukraine

Glyoxalase Centennial : 100 Years of Glyoxalase Research and Emergence of

Dicarbonyl Stress that hold on 2729 November 2013 at University of Warwick,

UK
http://www.biochemistry.org/Conferences/AllConferences/tabid/379/MeetingNo/SA158/view/Conference/Default.aspxhttp://www.biochemistry.org/Conferences/AllConferences/tabid/379/MeetingNo/SA158/view/Conference/Default.aspxhttp://www.biochemistry.org/Conferences/AllConferences/tabid/379/MeetingNo/SA158/view/Conference/Default.aspxhttp://www.biochemistry.org/Conferences/AllConferences/tabid/379/MeetingNo/SA158/view/Conference/Default.aspxhttp://www.biochemistry.org/Conferences/AllConferences/tabid/379/MeetingNo/SA158/view/Conference/Default.aspxhttp://www.biochemistry.org/Conferences/AllConferences/tabid/379/MeetingNo/SA158/view/Conference/Default.aspx


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C. TERTIARY SOURCES

Tertiary sources generally provide an overview or summary of a topic, and may

contain both primary and secondary sources. The information is displayed as entirely

factual, and does not include analysis or critique. Tertiary sources can also

be collections of primary and secondary sources, such as Dictionary, Encyclopedia,

databases, bibliographies and directories

1) Dictionary and Encyclopedia

The dictionary is a reference book that explains the meaning of

words. It serves to help a person get to know new words. In

addition to explaining the meaning of a Word, the dictionary may

also have a guideline, its origins (etymology) something words

and also an example of something for Word. For example

Biochemistry it means Science that deal with chemical the

living systems and its components aromatic amino acid it means

amino acids containing a benzene, etc.

2) Nomenclature

a. ENZYME

ENZYME is a repository of information relative to the nomenclature of enzymes.

It is primarily based on the recommendations of the Nomenclature Committee of the

International Union of Biochemistry and Molecular Biology (IUBMB) and it

describes each type of characterized enzyme for which an EC (Enzyme Commission)

number has been provided. (ExPASy)

b. Enzyme Nomenclature

Subtitle: "Recommendations of the Nomenclature Committee of the

International Union of Biochemistry and Molecular Biology on the Nomenclature

and Classification of Enzymes by the Reactions they Catalyse." Browse and searchfor enzyme names using EC numbers.

3) Database Bank

a. Binding Database

The BindingDB is a public database of measured binding affinities for

biomolecules, genetically or chemically modified biomolecules, and synthetic

compounds.The database currently contains data generated by isothermal titration

calorimetry, enzyme inhibition, and receptor-ligand binding methods

b. BioCyc Open Chemical Database
http://us.expasy.org/enzyme/http://www.bindingdb.org/http://biocyc.org/open-compounds.shtmlhttp://biocyc.org/open-compounds.shtmlhttp://www.bindingdb.org/http://us.expasy.org/enzyme/


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The BioCyc Open Chemical Database (BOCD) is a collection of chemical

compound data from the BioCyc databases. Most of the compounds act as substrates

in enzyme-catalyzed metabolic reactions, but some compounds serve as enzyme

activators, inhibitors, or cofactors. Chemical structures are provided for the majority

of compounds.

c. Biological Macromolecule Crystallization Database (BMCD)

The Biological Macromolecule Crystallization Database (BMCD) contains

crystal data and the crystallization conditions, which have been compiled from

literature. The current version of the BMCD includes 5247 crystal entries from

macromolecules for which diffraction quality crystals have been obtained. These

include proteins, protein:protein complexes, nucleic acid, nucleic acid:nucleic acid

complexes, protein:nucleic acid complexes, and viruses

d. BRENDA: Comprehensive Enzyme Information System

Free database containing information on over 3500 enzymes: nomenclature, EC

and registry numbers, reaction and specificity, inhibitors, structure, isolation,

literature references, etc. (Cologne University Bioinformatics Center)

e. Carcinogenic Potency Database

The Carcinogenic Potency Database (CPDB) is a unique and widely used

international resource of results from 6153 chronic, long-term animal cancer tests on

1485 chemicals. CPDB provides a standardized and easily accessible database with

qualitative and quantitative analyses of both positive and negative experiments that

have been published in the general literature through 1997 and by the National

Cancer Institute/National Toxicology Program through 1998. (UC Berkeley)

f. ChEMBL

"ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D

structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters,etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET

data)." (European Bioinformatics Institute)

g. DrugBank

"Bioinformatics and cheminformatics resource that combines detailed drug (i.e.

chemical, pharmacological and pharmaceutical) data with comprehensive drug target

(i.e. sequence, structure, and pathway) information." The database contains over

6700 drug entries including FDA-approved small molecule drugs, FDA-approved

biotech (protein/peptide) drugs, nutraceuticals and experimental drugs. Additionally,
http://xpdb.nist.gov:8060/BMCD4/index.faceshttp://www.brenda-enzymes.info/http://potency.berkeley.edu/cpdb.htmlhttp://potency.berkeley.edu/cpdb.htmlhttp://www.brenda-enzymes.info/http://xpdb.nist.gov:8060/BMCD4/index.faces


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non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are

linked to these drug entries. Each DrugCard entry contains drug/chemical data and

drug target or protein data. (Univ. of Alberta)

h. GenBank

GenBank is the NIH genetic sequence database, an annotated collection of all

publicly available DNA sequences.

i. Human Metabolome Database

"The Human Metabolome Database (HMDB) is a freely available electronic

database containing detailed information about small molecule metabolites found in

the human body. It is intended to be used for applications in metabolomics, clinical

chemistry, biomarker discovery and general education. The database is designed to

contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3)

molecular biology/biochemistry data."

j. PubChem

NIH cheminformatics database on biological activities of small molecules

primarily of interest to pharmaceutical and chemical genomics researchers.

PubChem includes substance information, compound structures, and BioActivity

data in three primary databases. The Substance/Compound database, where possible,

provides links to BioAssay description, literature, references, and assay data points.

PubChem is integrated with Entrez, NCBI's primary search engine, and also

provides compound neighboring, sub/superstructure, similarity structure,

BioActivity data, and other searching features. Links from PubChem's chemical

structure records to other Entrez databases provide information on biological

properties. These include links to PubMed scientific literature and NCBI's protein

3D structure resource. Links to depositor web sites provide further information.

(NIH does not take responsibility for the accuracy of the deposited data, and errorscan be rapidly propagated across multiple online databases.)

k. Nucleic Acid Database

Databases of 3D structural information on nucleic acids. (Rutgers University)

l. ZINC

Database of commercially-available compounds for virtual screening. ZINC

contains over 8 million compounds in ready-to-dock, 3D formats. (UC San

Francisco)

m. SCOP - Structural Classification of Proteins


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The SCOP database aims to provide a detailed and comprehensive description of

the structural and evolutionary relationships between all proteins whose structure is

known, including all entries in the Protein Data Bank (PDB). It is available as a set

of tightly linked hypertext documents which make the large database

comprehensible and accessible. In addition, the hypertext pages offer many

representations of proteins, including links to PDB entries, sequences, references,

images and interactive display systems.

n. National Center for Biotechnology Information (NCBI)

Parent site of the major NLM databases, including PubMed, GenBank,

Nucleotide and Protein Sequences, Protein Structures, Complete Genomes,

Taxonomy, PubChem, and others. (NIH)

o. GenomeNet

GenomeNet is a Japanese network of database and computational services for

genome research and related research areas in biomedical sciences, operated by the

Kyoto University Bioinformatics Center. It includes KEGG (Kyoto Encyclopedia of

Genes and Genomes), and other biochemical tools such as KEGG LIGAND.

4) BioChemical Network

a. Cheminformatics.org

Collection of links to cheminformatics programs and QSAR datasets (with

structures) in about 90 cheminformatics and CADD categories, with some similarity

searching tools.

b. Enzyme Explorer

Search by name, application, specificity or EC number. The Enzyme Explorer

also features detailed sites onmetabolic pathways, protein kinases, protease

specificity and inhibition, and glycoprotein analysis as well as new cell signaling,

analytical and diagnostic enzymes and reagents. (Sigma-Aldrich)c. ExPASy Proteomics Server

The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss

Institute of Bioinformatics is dedicated to the analysis of protein sequences and

structures. It provides access to a number of databases and tools useful for the

biological chemist, including UniProtKB and ENZYME, plus links to many others.

d. HapMap

"The goal of the International HapMap Project is to develop a haplotype map of

the human genome, the HapMap, which will describe the common patterns of human
http://cheminformatics.org/http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer.htmlhttp://www.sigmaaldrich.com/life-science/metabolomics/learning-center/metabolic-pathways.htmlhttp://us.expasy.org/http://hapmap.ncbi.nlm.nih.gov/http://hapmap.ncbi.nlm.nih.gov/http://us.expasy.org/http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/metabolic-pathways.htmlhttp://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer.htmlhttp://cheminformatics.org/


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DNA sequence variation. The HapMap is expected to be a key resource for

researchers to use to find genes affecting health, disease, and responses to drugs and

environmental factors." (NIH)

e. OSIRIS Property Explorer

Calculates on-the-fly drug-relevant properties (cLogP, solubility, MW) from a

valid structure. Prediction results are valued and color coded. (Actelion)

f. Protein Data Bank

The single international repository for the processing and distribution of 3D

structure data of biological macromolecules determined by X-ray crystallography

and NMR. The Research Collaboratory for Structural Bioinformatics is a non-profit

collaboration between Rutgers, SDSC and NIST.

g. Proteopedia

A wiki site that aims to collect, organize and disseminate structural and functional

knowledge about protein, RNA, DNA, and other macromolecules, and their

assemblies and interactions with small molecules.

h. STITCH: Chemical-Protein Interactions

"STITCH is a resource to explore known and predicted interactions of chemicals

and proteins. Chemicals are linked to other chemicals and proteins by evidence

derived from experiments, databases and the literature. STITCH contains

interactions for over 74,000 small molecules and over 2.5 million proteins in 630

organisms."

i. UniProt

UniProt (Universal Protein Resource) is a central repository of protein sequence

and function data, merging the information contained in Swiss-Prot, TrEMBL,

andPIR. The UniProt Knowledgebase (UniProtKB) is the central access point for

curated protein information, including function, classification, and cross-reference.The UniProt Reference Clusters (UniRef) databases combine closely related

sequences into a single record to speed searches. The UniProt Archive (UniParc) is a

repository reflecting the history of all protein sequences.
http://www.organic-chemistry.org/prog/peo/http://www.rcsb.org/pdb/http://www.proteopedia.org/http://stitch.embl.de/http://pir.uniprot.org/http://pir.georgetown.edu/http://pir.georgetown.edu/http://pir.uniprot.org/http://stitch.embl.de/http://www.proteopedia.org/http://www.rcsb.org/pdb/http://www.organic-chemistry.org/prog/peo/


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BAB III

CONCLUSION


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References :

Whiting, G.C (1970). "Sugars". In A.C. Hulme. The Biochemistry of Fruits and their

Products. Volume 1. London & New York: Academic Press. hlm. 1=31

http://www.lib.utexas.edu

http://id.wikipedia.org/wiki/Kamus

http://journal.biochemisty//.pdf

http://www.biochemweb.org/

http://id.wikipedia.org/wiki/Biokimia
http://www.lib.utexas.edu/http://www.biochemweb.org/http://id.wikipedia.org/wiki/Biokimiahttp://id.wikipedia.org/wiki/Biokimiahttp://www.biochemweb.org/http://www.lib.utexas.edu/

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