This document discusses proteins and amino acids. It defines proteins as large biomolecules composed of chains of amino acids that are essential to life processes. The 20 standard amino acids are the building blocks of proteins. They contain an amino group, a carboxyl group, a hydrogen atom, and a variable side chain that determines each amino acid's properties. Proteins have primary, secondary, tertiary, and quaternary structures that give them their final 3D shapes and functions in the body.
Proteins are the macromolecules responsible for the biological processes in the cell. They consist at their most basic level of a chain of amino acids, determined by the sequence of nucleotides in a gene. Depending on the amino acid sequence (different amino acids have different biochemical properties) and interactions with their environment, proteins fold into a three-dimensional structure, which allows them to interact with other proteins and molecules and perform their function
Proteins are the macromolecules responsible for the biological processes in the cell. They consist at their most basic level of a chain of amino acids, determined by the sequence of nucleotides in a gene. Depending on the amino acid sequence (different amino acids have different biochemical properties) and interactions with their environment, proteins fold into a three-dimensional structure, which allows them to interact with other proteins and molecules and perform their function
Amino acids are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues.Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.
Amino acids are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues.Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.
This was a report regarding amino acids and peptides that was prepared by our group and this report made in order to make a score. Hope this slide makes more it to be on help.
Introduction to protein , Structure of Amino acid, Asymmetric carbon, Nomenclature of amino acid, Classification of amino acid, Properties & functions of amino acids, Definition of protein, Peptide bond
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.
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.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
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.
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 .
1. Dr. Ifat Ara Begum
Assistant Professor
Dept of Biochemistry
Dhaka Medical College
2.
3. Large molecules
Made up of chains of amino acids
Are found in every cell in the body
Are involved in most of the body’s
functions and life processes
The sequence of amino acids is
determined by DNA
4. Greek word, “PROTEIOS” , means,
“Holding the first place”. Swedish chemist
Berzelius suggested the name.
Most abundant molecule of living system
& constitute about 50% of cellular dry
weight.
5. First protein to be sequenced: Insulin.
Frederick Sanger won noble prize for
this achievement in 1958
8. Amino acid has a central carbon atom to which
4 diff groups of atoms are attached:
An Amino group (NH2)
A Carboxylic acid group (COOH)
A Hydrogen atom (H)
A Radical or R group: H, CH3, CH3-CH2 etc
which determines its properties and functions in
protein.
9. The acidic and basic properties of NH2 &
COOH groups make the AA molecule
“Amphoteric”.
Primary amino acid
L- α type, i.e. the amino group is usually
attached with the α carbon and placed on
left side with respect to spatial
configuration.
10.
11. All AAs (except glycine) show optical
isomerism & optical activity as they have
at least 1 asymmetric carbon.
12. Nomenclature: By the first three
letters of their name. e.g. Serine (ser)
Exception:
Tryptophan (Trp), Isoleucine (Ile)
Asparagine (Asn) & Glutamine (Gln)
13. Based on structure of side chain (R) &
their reaction in solution:
Acidic/ Mono amino di carboxylic Acid:
Asp, Glu.
Basic/ Di amino mono carboxylic Acid:
Lys, Arg, His.
Neutral/ Mono amino mono carboxylic
Acid: Rest 15 AAs. e.g. Ala, Tyr, Trp, Cys, Met,
etc.
14. Based on polarity of side chain (R) :
Polar Amino Acid: Have hydrophilic side
chain with/without charge. e.g. Acidic AA
(negative charge), Basic AA (positive
charge), Other AAs like Gly, Ser, Thr, Tyr,
Cys, Gln, Asn are of without charge.
Non-polar Amino Acid: Have hydrophobic
side chain with no charge. e.g. Rest 8 AAs.
15. Nutritional classification of Amino Acid:
Essential/Indispensable AA: 8 in number.
e.g. Phe, Val, Trp, Thr, Ile, Met, Leu, Lys.
Semi essential AA: 2 in number. e.g. Arg, His.
Needed for children.
Non-essential/ Dispensable AA: Rest 10 AAs.
e.g. Asp, Glu, Cys, Ser, Gly, Ala, Asn, Gln, Tyr,
Pro.
16.
17. Within the body, Tyrosine and Cystine
are synthesized from the EAA-Phenylalanine
& Methionine
respectively. So, Tyr & Cys may
become EAA if the dietary supply of
Phe & Met is reduced or absent.
18. Metabolic Classification of Amino Acid
(Based on their catabolic fate):
Glucogenic/Glycogenic AA: AA having C
skeleton possessing metabolic potential to
produce glucose. e.g. Gly, Ala, Glu, Gln, Val
etc.
Ketogenic AA: AA having ……ketone
bodies. e.g. Leu, Lys.
Both glucogenic & ketogenic AA: Phe,
Tyr, Trp, Ile.
19.
20. Physical : Colorless, Crystalline, water soluble,
high melting point (>200 degree C),
stereoisomerism (D-L isomers, optical isomers)
& optical activity.
Chemical :
Act as ampholytes (COOH group acts as acidic
group by donating proton and NH2 group acts
as basic group by accepting proton).
21. Acts as buffer and have definite iso-electric
PHH (( PH at which molecules carry
no net charge).
Forms salts with acid or base by reacting
with NH2 or COOH group respectively.
Forms esters with alcohol.
Forms carbamino compounds with CO2.
22. Gives color reaction with ninhydrine.
Undergo acetylation & amidation
reaction due to NH2 group.
23. 1. Act as building block of peptides,
polypeptides & proteins.
[Arbitrarily peptide, polypeptide & protein
are made of 2-10 AAs, 10-100 AAs &
>100 AAs respectively.]
24. 2. Supports gluconeogenesis in fasting &
starvation.
3. Participates in synthesis of specialized
products. e.g. neurotransmitters,
hormones, purine, pyrimidine, heme, etc.
4. Source of S (Cys/Met) /Methyl group
(Met) in body.
25. Definition:
Macromolecular polymer of Amino Acids
linked together by peptide bond.
Minimum molecular weight: 5000-8000
Number of amino acid: >100
Elementary Composition of protein:
C, O, N, H, S in different percentages.
26. Covalent bond formed by joining the –
COOH group of one amino acid and
the –NH2 group of another amino
acid with removal of one molecule of
water.
27.
28. Covalent bond, i.e. sharing of electron
pair.
Shows partial double bond character
Rigid, planer & do not rotate.
Not broken by denaturing agent
Broken by proteolytic enzymes.
29. Types of protein Function Example
Structural Protein Support framework of
cell
Collagen, Elastin, etc
Catalytic Protein Catalysis Enzymes
Transport Protein Transport of
substances
Albumin, Transferrin
Hormonal Protein Regulation of
functions
Insulin, Glucagon
Gene regulatory
Protein
Regulate genetic
functions
Histone, Protamine
Protective Protein Prevent infection Immunoglobulin
Receptor Protein Receptor function LDL receptor
Contractile Protein Muscle contraction Actin, Myosin
30. 1. Simple Protein: Contains only AAs without any
non-protein substances.
Fibrous protein/scleroprotein: Fibre like, animal
origin, possess high tensile strength, water insoluble
& highly resistant to proteolytic enzymes. Chief
component of tendon, ligaments, cartilage, hair,
nail, etc. Example: Collagen, Elastin, keratin, etc.
Globular protein: oval/spherical in shape, water
soluble, digestible. Example: Albumin, Globulin,
Histone, etc.
31. 2. Conjugated Protein: Composed of simple
protein along with non-protein prosthetic substances.
Example:
Nucleoprotein: Nucleohistones (Nucleic acid)
Lipoprotein: VLDL, HDL, etc (Lipid)
Glycoprotein: Mucin (Carbohydrates)
Chromatoprotein: Hemoglobin, cytochrome (Heme)
Metalloprotein: Ceruloplasmin (Cu), Carbonic
anhydrase (Zn) etc.
32. 3. Derived Protein: Denatured/degraded
products of simple/conjugated proteins.
Protein → Protean → Metaprotein → Proteose
→Peptone → Peptides → Amino Acids.
[Protean, Metaprotein → Primary derived
protein as no/little change in peptide bond,
Rest are secondary derived proteins
produced by progressive hydrolytic cleavage of
peptide bonds. ]
33. Complete Proteins: Contains all EAAs
in proportion required for body. Example:
Egg albumin, Meat etc.
Incomplete Proteins: Lacks 1/more
EAAs. Example: Gelatin.
Partially incomplete Proteins:
Partially lacks 1/more EAAs.
34. Proteins are abundant in
◦Dairy foods
◦ Meats
◦Poultry
◦ Meat alternatives such as dried
beans, peanut butter, nuts, and soy
35. A well-balanced diet can meet daily
protein needs
Most people consume adequate protein
from their diet and do not need protein
supplements
36. Isoelectric point of protein
Colloidal properties
Protein denaturation
Protein precipitation
Protein sedimentation
Protein hydrolysis
Color reaction
UV light absorption
37. Isoelectric point, pI, is the pH
of an aqueous solution of an
amino acid (or protein) at which
the molecules on average have
no net charge. 。
38.
39. Any alteration in the
structure or sequencing
changes the shape and
function of the protein
40. Primary structure: Exact sequence
of AAs held together by peptide
bonds in peptide chain. It is
determined genetically and this in
turns determines secondary, tertiary
& quaternary structures. Example:
Insulin.
41.
42. Secondary structure: Helical or
pleated sheet like conformation
produced by a definite, periodic
folding, twisting or coiling of primary
structure. Hydrogen bond is present
here Example: fibrous protein
(collagen, elastin, keratin) .
43. α helix: Most common and stable
conformation for a PP chain
Spiral structure
Right handed
Stabilized by H-bond
Distance between AAs are 1.5 degree
A
45. β pleated sheet: PP chains are
almost fully extended.
Distance between AAs are 3.5
degree A
Stabilized by H-bond
Major structural motif of protein.
46.
47. Adjacent strands in a sheet can run in
the same direction with regard to the
amino and carboxyl ends of PP chain
or in opposite direction.
48.
49.
50. Tertiary Protein: Three dimensional
globular form of protein produced by further
folding and twisting of secondary structure
about itself with the hydrophobic side chains
buried interiorly and hydrophilic groups
exposed outside. It is stabilized by hydrogen
bond, disulfide bond, ionic interaction and
hydrophobic interactions. Example:
albumin, globulin, antibody etc.
55. 1. Hydrogen bond
2. Electrostatic interaction
3. Hydrophobic interaction
4. van der waals force
5. Disulfide bond
56. A.三级结构中的作用力
1. Disulfide bond 2. Electrostatic interaction
3. Hydrogen bond 4. Hydrophobic interaction
57. The unfolding and disorganization of
protein’s secondary, tertiary & quaternary
structures, which are accompanied by
hydrolysis of sulfide and hydrogen bond
but not accompanied by hydrolysis of
peptide bond.
58. Denaturing agents: Heat, Organic
solvents, Mechanical mixing, Strong
acid/base, Detergents, Ions of heavy
metals, e.g. lead, mercury etc.
60. Formation of cytoskeleton (Flexible structural
framework for cell/tissues)
Provides mechanical support (by structural
protein), defense against infection (by
antibody)
Acts as vehicle for transport of diff molecules
Provide COP
Have function as receptors and maintains the
homeostasis of the body.
61. Muscle contraction
Source of energy
Helps in coagulation
Acts as buffer
Promote catalytic function & hormonal
function
Genetic information-storage, expression &
transmission etc.
