This chapter discusses amino acids, peptides, and proteins. It covers the structure and properties of amino acids, how they combine to form peptides and proteins, and the various functions of proteins, including catalysis, transport, structure, and motion. Methods for analyzing, separating, and purifying proteins are also described, such as ion exchange chromatography, size exclusion chromatography, electrophoresis, and protein sequencing. Finally, the chapter classifies common amino acids based on the properties of their variable side chains.
Laboratory method for measuring enzyme activity.
Vital for study of enzyme kinetics and enzyme inhibition.
Measurement of enzyme activity – follow the change in concentration of substrate or product – measure reaction rate.
Laboratory method for measuring enzyme activity.
Vital for study of enzyme kinetics and enzyme inhibition.
Measurement of enzyme activity – follow the change in concentration of substrate or product – measure reaction rate.
Content :-
What is porphyrin?
Biosynthesis of porphyrin (heme)
Site
Reactions
Regulation
Degradation of heme
Site
Reactions
Reference
What is Porphyrin?
Porphyrins are cyclic compound formed by the linkage of four pyrrole rings through methyne(=HC-)bridges.
Structure of hemoglobin & chlorophyll
Examples of some important humanand animal hemoproteins.
Biosynthesis of heme
Site of biosynthesis:-
-Liver (hepatocyte) & Bone Marrow
( erythryoid producing cells )
2) ALA dehydratase :-
The substrates are two molecules of ALA.
The product is porphobilinogen, the first pyrrole.
ALA dehydratase is a -SH containing enzyme.
It is very susceptible to inhibition by lead.
3) Uroporphyrinogen I synthase and uroporphyrinogen IIIcosynthase
Production of uroporphyrinogen III requires two enzymes.The substrates are four molecules of porphobilinogen.
4) Uroporphyrinogen decarboxylase:-
Decarboxylates the acetic acid groups, converting them to methyl groups.
5) Coproporphyrinogen III oxidase:-
Catalyzes the conversion of two propionic acid groups to vinyl groups
6) Protoporphyrinogen IX oxidase:-
Protoporphyrinogen IX oxidase converts the methylene bridges between the pyrrole rings to methenyl bridges.
7) Ferrochelatase:-
Ferrochelatase adds Fe++ to protoporphyrin IX, forming heme.
• The enzyme requires Fe++, ascorbic acid and cysteine (reducing agents).
• Ferrochelatase is inhibited by lead.
Regulation of heme synthesis
Feedback regulation:- heme is a feedback inhibitor of ALA synthase. ALA synthase occurs in both hepatic (ALAS 1) and erythroid (ALAS 2) forms.
Effects of drugs and steroids:- Certain drugs and steroids can increase heme synthesis via increased production of the ratelimiting enzyme, ALA synthase
Substrate availability:- Fe++ must be available for ferrochelatase.
Degradation of heme
Site of Degradation :-
- cells of the reticulo endothelial system in spleen, liver and bone marrow
Heme Degradation
Most of the heme which is degraded comes from hemoglobin in red blood cells, which have a life span of about 120 days.
There is thus a turnover of about 6 g/day of hemoglobin.
Normally , senescent red blood cells and heme from other sources are engulfed by cells of the reticuloendothelial system.
The globin is recycled or converted into amino acids, which in turn are recycled or catabolized as required.
Heme is oxidized.
Microsomal heme oxygenase system
Transport of bilirubin in Plasma
Bilirubin on release from macrophages circulates as unconjugated bilirubin in plasma tightly bound to albumin.
HARPER’S ILLUSTRATED BIOCHEMISTRY (28TH EDITION) by robert murray,david A.bender,peter j kennekky,victor w rodwell,p.antony weil.(page No-271)
Biochemistry Lippincott’s Illustrated Reviews by Richard Harvey& Denise Ferrier
Enzymes are biological molecules (typically proteins) that significantly speed up the rate of virtually all of the chemical reactions that take place within cells. They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism
Introduction-Cell wall and functions
Gram +ve and -ve cell wall
Bacterial cell wall - structure
Peptidoglycan-Composition and Structure
Types of polysaccharidesBacterial cell wall
Functions of polysaccharides in Bacterial cell wall
This Course is included in the syllabus of Bachelor in Science Agriculture level study in Tribhuvan University. The course belongs to 1h lecture.This slide include general introduction of amino acid. It describes about structure, function , type and role of amino acid.
Active sites of the enzyme is that point where substrate molecule bind for the chemical reaction. It is generally found on the surface of enzyme and in some enzyme it is a “Pit” like structure
The active site is a three-dimensional cleft formed by groups that come from different parts of the amino acid sequence
The active site takes up a relatively small part of the total volume of an enzyme
Active sites are clefts or crevices
Substrates are bound to enzymes by multiple weak attractions.
The specificity of binding depends on the precisely defined arrangement of atoms in an active site.
Content :-
What is porphyrin?
Biosynthesis of porphyrin (heme)
Site
Reactions
Regulation
Degradation of heme
Site
Reactions
Reference
What is Porphyrin?
Porphyrins are cyclic compound formed by the linkage of four pyrrole rings through methyne(=HC-)bridges.
Structure of hemoglobin & chlorophyll
Examples of some important humanand animal hemoproteins.
Biosynthesis of heme
Site of biosynthesis:-
-Liver (hepatocyte) & Bone Marrow
( erythryoid producing cells )
2) ALA dehydratase :-
The substrates are two molecules of ALA.
The product is porphobilinogen, the first pyrrole.
ALA dehydratase is a -SH containing enzyme.
It is very susceptible to inhibition by lead.
3) Uroporphyrinogen I synthase and uroporphyrinogen IIIcosynthase
Production of uroporphyrinogen III requires two enzymes.The substrates are four molecules of porphobilinogen.
4) Uroporphyrinogen decarboxylase:-
Decarboxylates the acetic acid groups, converting them to methyl groups.
5) Coproporphyrinogen III oxidase:-
Catalyzes the conversion of two propionic acid groups to vinyl groups
6) Protoporphyrinogen IX oxidase:-
Protoporphyrinogen IX oxidase converts the methylene bridges between the pyrrole rings to methenyl bridges.
7) Ferrochelatase:-
Ferrochelatase adds Fe++ to protoporphyrin IX, forming heme.
• The enzyme requires Fe++, ascorbic acid and cysteine (reducing agents).
• Ferrochelatase is inhibited by lead.
Regulation of heme synthesis
Feedback regulation:- heme is a feedback inhibitor of ALA synthase. ALA synthase occurs in both hepatic (ALAS 1) and erythroid (ALAS 2) forms.
Effects of drugs and steroids:- Certain drugs and steroids can increase heme synthesis via increased production of the ratelimiting enzyme, ALA synthase
Substrate availability:- Fe++ must be available for ferrochelatase.
Degradation of heme
Site of Degradation :-
- cells of the reticulo endothelial system in spleen, liver and bone marrow
Heme Degradation
Most of the heme which is degraded comes from hemoglobin in red blood cells, which have a life span of about 120 days.
There is thus a turnover of about 6 g/day of hemoglobin.
Normally , senescent red blood cells and heme from other sources are engulfed by cells of the reticuloendothelial system.
The globin is recycled or converted into amino acids, which in turn are recycled or catabolized as required.
Heme is oxidized.
Microsomal heme oxygenase system
Transport of bilirubin in Plasma
Bilirubin on release from macrophages circulates as unconjugated bilirubin in plasma tightly bound to albumin.
HARPER’S ILLUSTRATED BIOCHEMISTRY (28TH EDITION) by robert murray,david A.bender,peter j kennekky,victor w rodwell,p.antony weil.(page No-271)
Biochemistry Lippincott’s Illustrated Reviews by Richard Harvey& Denise Ferrier
Enzymes are biological molecules (typically proteins) that significantly speed up the rate of virtually all of the chemical reactions that take place within cells. They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism
Introduction-Cell wall and functions
Gram +ve and -ve cell wall
Bacterial cell wall - structure
Peptidoglycan-Composition and Structure
Types of polysaccharidesBacterial cell wall
Functions of polysaccharides in Bacterial cell wall
This Course is included in the syllabus of Bachelor in Science Agriculture level study in Tribhuvan University. The course belongs to 1h lecture.This slide include general introduction of amino acid. It describes about structure, function , type and role of amino acid.
Active sites of the enzyme is that point where substrate molecule bind for the chemical reaction. It is generally found on the surface of enzyme and in some enzyme it is a “Pit” like structure
The active site is a three-dimensional cleft formed by groups that come from different parts of the amino acid sequence
The active site takes up a relatively small part of the total volume of an enzyme
Active sites are clefts or crevices
Substrates are bound to enzymes by multiple weak attractions.
The specificity of binding depends on the precisely defined arrangement of atoms in an active site.
Describes the structural organisation of proteins with example and its determination, interrelationship b/w structure and function of proteins, also biologically important peptides is covered.
by Dr. N. Sivaranjani, MD
Amino acids are the units of proteins, and understanding its chemistry and the the properties assists in understanding the functions of proteins. This gives in an idea to why a certain protein behaves in a certain way.
Generative AI Deep Dive: Advancing from Proof of Concept to ProductionAggregage
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zkStudyClub - Reef: Fast Succinct Non-Interactive Zero-Knowledge Regex ProofsAlex Pruden
This paper presents Reef, a system for generating publicly verifiable succinct non-interactive zero-knowledge proofs that a committed document matches or does not match a regular expression. We describe applications such as proving the strength of passwords, the provenance of email despite redactions, the validity of oblivious DNS queries, and the existence of mutations in DNA. Reef supports the Perl Compatible Regular Expression syntax, including wildcards, alternation, ranges, capture groups, Kleene star, negations, and lookarounds. Reef introduces a new type of automata, Skipping Alternating Finite Automata (SAFA), that skips irrelevant parts of a document when producing proofs without undermining soundness, and instantiates SAFA with a lookup argument. Our experimental evaluation confirms that Reef can generate proofs for documents with 32M characters; the proofs are small and cheap to verify (under a second).
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UiPath Test Automation using UiPath Test Suite series, part 5DianaGray10
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End-to-end overview of CI/CD pipeline with Azure devops
Speaker:
Lyndsey Byblow, Test Suite Sales Engineer @ UiPath, Inc.
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
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My slides at Nordic Testing Days 6.6.2024
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The Art of the Pitch: WordPress Relationships and Sales
amino asid,peptides and proteins
1. CHAPTER 3
Amino Acids, Peptides,
Proteins
• Structure and naming of amino acids
• Structure and properties of peptides
• Ionization behavior of amino acids and peptides
• Purification and assay methods
• Peptide sequencing and chemical synthesis
• Protein sequence analysis
2. Proteins: Main Agents of
Biological Function
• Catalysis:
–enolase (in the glycolytic pathway)
–DNA polymerase (in DNA replication)
• Transport:
–hemoglobin (transports O2 in the blood)
–lactose permease (transports lactose across the cell membrane)
• Structure:
–collagen (connective tissue)
–keratin (hair, nails, feathers, horns)
• Motion:
–myosin (muscle tissue)
–actin (muscle tissue, cell motility)
3. Amino Acids: Building Blocks of
Protein
• Proteins are heteropolymers of α-amino acids
• Amino acids have properties that are well
suited to carry out a variety of biological
functions:
– Capacity to polymerize
– Useful acid-base properties
– Varied physical properties
– Varied chemical functionality
4. Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation: start from
α-carbon and go down the R-group
5. Most α-Amino Acids are Chiral
• The α-carbon has always
four substituents and is
tetrahedral
• All (except proline) have an
acidic carboxyl group, a
basic amino group, and an
alpha hydrogen connected
to the α-carbon
• Each amino acid has an
unique fourth substituent R
• In glycine, the fourth
substituent is also hydrogen
6. Amino Acids: Classification
Common amino acids can be placed in five
basic groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
13. Not incorporated by ribosomes
Arise by post-translational modifications of
proteins
Reversible modifications, esp.
phosphorylation is important in regulation
and signaling
Uncommon Amino
Acids in Proteins
15. Ionization
At acidic pH, the carboxyl
group is protonated
and the amino acid is
in the cationic form
At neutral pH, the
carboxyl group is
deprotonated but the
amino group is
protonated. The net
charge is zero; such
ions are called
Zwitterions
At alkaline pH, the amino
group is neutral –NH2
and the amino acid is
in the anionic form.
16. Substituent effects on pKa Values
α-carboxy group is much more acidic than in carboxylic acids
α-amino group is slightly less basic than in amines
17. Amino Acids Can
Act as Buffers
Amino acids with
uncharged side-chains,
such as glycine, have two
pKa values:
The pKa of the α-carboxyl
group is 2.34
The pKa of the α-amino
group is 9.6
It can act as a buffer in
two pH regimes.
18. Amino Acids Carry a Net Charge
of Zero at a Specific pH
•Zwitterions predominate at pH values between the pKa values
of amino and carboxyl group
•For amino acid without ionizable side chains, the Isoelectric
Point (equivalence point, pI) is
• At this point, the net charge is zero
– AA is least soluble in water
– AA does not migrate in electric field
2
21 pKpK
pI
+
=
19. Ionizable Side Chains Can Show
Up in Titration Curves
• Ionizable side chains
can be also titrated
• Titration curves are
now more complex
• pKa values are
discernable if two pKa
values are more than
two pH units apart
Why is the side-chain
pK so much higher?
20. How to Calculate the pI When the
Side-chain is Ionizable?
• Identify species that carries
a net zero charge
• Identify pKa value that
defines the acid strength of
this zwitterion: (pK2)
• Identify pKa value that
defines the base strength of
this zwitterion: (pKR)
• Take the average of these
two pKa values
21. Peptides and Peptide bonds
Peptide bond in
a di-peptide
“Peptides” are
small
condensation
products of
amino acids
They are “small”
compared to
proteins (di, tri,
tetra… oligo-)
22. Peptide Ends are Not the Same
Numbering starts from the amino terminus
AA1 AA2 AA3 AA4 AA5
23. The Three Letter Code
• Naming starts from
the N-terminus
• Sequence is written
as:
Ala-Glu-Gly-Lys
• Sometimes the one-
letter code is used:
AEGK
24. Peptides: A Variety of Functions
• Hormones and pheromones:
– insulin (think sugar)
– oxytocin (think childbirth)
– sex-peptide (think fruit fly mating)
• Neuropeptides
– substance P (pain mediator)
• Antibiotics:
– polymyxin B (for Gram - bacteria)
– bacitracin (for Gram + bacteria)
• Protection, e.g. toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)
25. Proteins are:
• Cofactor is a general term for functional non-amino acid component
– Metal ions or organic molecules
• Coenzyme is used to designate an organic cofactors
– NAD+
in lactate dehydrogenase
• Prosthetic groups are covalently attached cofactors
– Heme in myoglobin
• Polypeptides (covalently linked α-amino acids) + possibly –
• cofactors,
• coenzymes,
• prosthetic groups,
• other modifications
28. Peptides and Proteins-
Burning Questions
Sequence and composition?
Three-dimensional structure?
Folding Mechanism?
Biochemical role?
Functional regulation?
Molecular interactions with small and macro-molecules?
Structural and sequence relatives?
Cellular and sub-cellular localization?
Physical and chemical properties?
29. Purification – Fractionation of
Protein Mixtures
• Separation relies on differences in physico-
chemical properties
– Solubility – Selective Precipitation (Centrifugation)
– Thermal stability --
– Charge --Electrophoresis, Isoelectric Focusing, IEC
– Size – Dialysis, Sedimentation (Centrifugation), GFC
– Affinity for a ligand – “Pull down” assays (Centrifugation),
AC
– Hydrophobicity (HIC)
• Chromatography is commonly used for
preparative separation
34. Electrophoresis for Protein
Analysis
Separation in
analytical scale is
commonly done by
electrophoresis
– Electric field pulls
proteins according to
their charge
– Gel matrix hinders
mobility of proteins
according to their
size and shape
35. SDS PAGE: Molecular Weight
• SDS – sodium dodecyl
sulfate – a detergent
• SDS micelles binds to,
and unfold all the
proteins
– SDS gives all proteins an
uniformly negative
charge
– The native shape of
proteins does not matter
– Rate of movement will
only depend on size:
small proteins will move
faster
-
37. Spectroscopic Detection of Aromatic
Amino Acids
• The aromatic amino acids
absorb light in the UV
region
• Proteins typically have
UV absorbance maxima
around 275-280 nm
• Tryptophan and tyrosine
are the strongest
chromophores
• Concentration can be
determined by UV-visible
spectrophotometry using
Beers law: A = ε·c·l
38. Chapter 3: Summary
In this chapter, we learned about:
• The many biological functions of peptides and
proteins
• The structures and names of amino acids found in
proteins
• The ionization properties of amino acids and
peptides
• The methods for separation and analysis of
proteins
FIGURE 3-16 Column chromatography. The standard elements of a chromatographic column include a solid, porous material (matrix) supported inside a column, generally made of plastic or glass. A solution, the mobile phase, flows through the matrix, the stationary phase. The solution that passes out of the column at the bottom (the effluent) is constantly replaced by solution supplied from a reservoir at the top. The protein solution to be separated is layered on top of the column and allowed to percolate into the solid matrix. Additional solution is added on top. The protein solution forms a band within the mobile phase that is initially the depth of the protein solution applied to the column. As proteins migrate through the column, they are retarded to different degrees by their different interactions with the matrix material. The overall protein band thus widens as it moves through the column. Individual types of proteins (such as A, B, and C, shown in blue, red, and green) gradually separate from each other, forming bands within the broader protein band. Separation improves (i.e., resolution increases) as the length of the column increases. However, each individual protein band also broadens with time due to diffusional spreading, a process that decreases resolution. In this example, protein A is well separated from B and C, but diffusional spreading prevents complete separation of B and C under these conditions.
In this case the effect of charge is eliminated by binding a negatively charged detergent, SDS, to all the proteins which are denatured. The SDS binds uniformly per unit length of protein and therefore the force on the molecules from the field will be a uniform amount per unit length and the only affect on the speed of travel will be the retarding force due to their size. This is therefore a method to separate molecules based on their molecular weights. Clearly not useful for oligomers since these will be forced apart by the SDS.