Proteins undergo several key processes that are important for their proper function in cells. These include protein maturation, which involves proper folding with the help of chaperone proteins, and post-translational modifications that can impact protein localization, activity, and interactions. Other important concepts are protein sorting, transport and insertion in cellular membranes, activation and inactivation mechanisms for regulating function, and degradation pathways that remove damaged or unneeded proteins. Understanding these protein basics is fundamental for molecular biology and biochemistry.
Biochemistry of Metabolic Pathways: From Energy Production to Disease Mechanismshealthcare360social
In this guide, We’ll explore how the Biochemistry of metabolic pathways fuel our bodies, build essential molecules, and even play a role in health and disease
Introduction
Protein modifications
Folding
Chaperon mediated
Enzymatic
Cleavage
Addition of functional groups
Chemical groups
Hydrophobic groups
Proteolysis
Conclusion
Reference
Post translation control-regulation_of_gene_expression_in_eukaryotes - copyDhruviSuvagiya
Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones.
Biochemistry of Metabolic Pathways: From Energy Production to Disease Mechanismshealthcare360social
In this guide, We’ll explore how the Biochemistry of metabolic pathways fuel our bodies, build essential molecules, and even play a role in health and disease
Introduction
Protein modifications
Folding
Chaperon mediated
Enzymatic
Cleavage
Addition of functional groups
Chemical groups
Hydrophobic groups
Proteolysis
Conclusion
Reference
Post translation control-regulation_of_gene_expression_in_eukaryotes - copyDhruviSuvagiya
Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones.
Leftover proteins, also known as protein remnants or protein degradation products, refer to the fragments or remnants remaining after the degradation of proteins during various cellular processes. These leftover proteins typically consist of partially hydrolyzed peptides and individual amino acids generated through proteolytic cleavage
DOWNLOAD THE POWERPOINT FILE HERE:
https://www.dropbox.com/s/3izi11rbc7axri3/CHE-109.pptx?dl=0
A presentation slide on Peptides and Proteins. Presented in the Course CHE-109 in East West University.
Post translation modifications(molecular biology)IndrajaDoradla
description of post translation modifications which include folding,proteolytic clevage and chemical modification and protein splicing and protein degradation
Metabolomics-Introduction, metabolism, intermediary metabolism, metabolic pathways, metabolites, metabolome, metabolic turnover, techniques used in metabolomics, metabolite profiling methods, data analysis, metabolomic resources, role of metabolomics in system biology.
PROTEINS: Proteins are the organic compounds made of amino acids and joined together by peptide bonds.
PEPTIDES: These are short polymers formed from the linking in a defined order of amino acids.
Protein and peptides are the most abundant material which act as hormones, transport protein, structural protein, receptor, immunoglobulin’s in living system and biological cell.
Protein and peptides are important part in several metabolic process, immunogenic defense and many other biological activities.
Protein and peptide use in the treatment of various diseases including Endocrine dysfunction, Infection diseases, Cancer, and CNS disorders.
According to their biological roles
Enzymes- Catalyses virtually all chemical reaction
Transport proteins i.e. Haemoglobin of erythrocytes
Defense proteins i.e. Immuno globulins Antibodies
Structural proteins i.e. Collagen in bones
Regulatory proteins i.e. insulin
Nutrient and storage proteins i.e. ovalbumin
According to their solubility
Globular proteins: Soluble in Water
Fibrous proteins: Insoluble in water
WHY PROTEN AND PEPTIDE DRUGS?
The protein and peptide are very important in biological cells.
Lack of proteins and peptides causes diseases like Diabetes mellitus.
Diabetes mellitus is cause due to the lack of protein called INSULIN.
Now a day R-DNA technology and hybridoma also use in protein and peptide based pharmaceuticals.
FUNCTIONS
Transport and storage of small molecules.
Coordinated motion via muscle contraction.
Mechanical support from fibrous protein.
Generation and transmission of nerve impulses.
Enzymatic catalysis.
Immune protection through antibodies.
Control of growth and differentiation via hormones.
Problems with proteins
Elimination by B and T cells.
Proteolysis by endo/exo peptidases.
Small proteins filtered out by the kidneys very quickly.
Unwanted allergic reactions may develop (even toxicity).
Loss due to insolubility/adsorption.
"Bacterial metabolism: Fueling life's processes in tiny powerhouses."
Use of bacterial metabolism in biotechnology, biofuels, and other industries
Examples of how bacterial metabolism is harnessed for beneficial purposes
"Metabolism: the sum of chemical reactions in an organism, supporting growth, energy production, and vital functions."
"Bacterial Metabolism and Life: Pervading every aspect of life, shaping ecosystems, and influencing our world."
Bacterial metabolism refers to the collective chemical reactions and processes that occur within bacterial cells, enabling them to maintain life, grow, and reproduce. These metabolic activities involve a complex network of biochemical pathways that facilitate the conversion of nutrients into energy, biomolecules, and essential compounds necessary for bacterial survival.
Metabolic processes in bacteria include catabolic pathways that break down complex molecules (such as sugars) to release energy and anabolic pathways that build complex molecules (such as proteins, nucleic acids) using energy. Bacteria utilize various metabolic strategies based on their energy and carbon sources, including aerobic and anaerobic respiration, fermentation, and photosynthesis in photosynthetic bacteria.
The primary goals of bacterial metabolism are to obtain energy, synthesize necessary cellular components, regulate chemical processes, and adapt to changing environmental conditions. The understanding of bacterial metabolism is crucial for various fields, including medicine, agriculture, biotechnology, and environmental science, as it allows us to develop strategies to combat harmful bacteria, harness their metabolic capabilities for beneficial applications, and study their role in ecological systems.
Safalta Digital marketing institute in Noida, provide complete applications that encompass a huge range of virtual advertising and marketing additives, which includes search engine optimization, virtual communication advertising, pay-per-click on marketing, content material advertising, internet analytics, and greater. These university courses are designed for students who possess a comprehensive understanding of virtual marketing strategies and attributes.Safalta Digital Marketing Institute in Noida is a first choice for young individuals or students who are looking to start their careers in the field of digital advertising. The institute gives specialized courses designed and certification.
for beginners, providing thorough training in areas such as SEO, digital communication marketing, and PPC training in Noida. After finishing the program, students receive the certifications recognised by top different universitie, setting a strong foundation for a successful career in digital marketing.
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Leftover proteins, also known as protein remnants or protein degradation products, refer to the fragments or remnants remaining after the degradation of proteins during various cellular processes. These leftover proteins typically consist of partially hydrolyzed peptides and individual amino acids generated through proteolytic cleavage
DOWNLOAD THE POWERPOINT FILE HERE:
https://www.dropbox.com/s/3izi11rbc7axri3/CHE-109.pptx?dl=0
A presentation slide on Peptides and Proteins. Presented in the Course CHE-109 in East West University.
Post translation modifications(molecular biology)IndrajaDoradla
description of post translation modifications which include folding,proteolytic clevage and chemical modification and protein splicing and protein degradation
Metabolomics-Introduction, metabolism, intermediary metabolism, metabolic pathways, metabolites, metabolome, metabolic turnover, techniques used in metabolomics, metabolite profiling methods, data analysis, metabolomic resources, role of metabolomics in system biology.
PROTEINS: Proteins are the organic compounds made of amino acids and joined together by peptide bonds.
PEPTIDES: These are short polymers formed from the linking in a defined order of amino acids.
Protein and peptides are the most abundant material which act as hormones, transport protein, structural protein, receptor, immunoglobulin’s in living system and biological cell.
Protein and peptides are important part in several metabolic process, immunogenic defense and many other biological activities.
Protein and peptide use in the treatment of various diseases including Endocrine dysfunction, Infection diseases, Cancer, and CNS disorders.
According to their biological roles
Enzymes- Catalyses virtually all chemical reaction
Transport proteins i.e. Haemoglobin of erythrocytes
Defense proteins i.e. Immuno globulins Antibodies
Structural proteins i.e. Collagen in bones
Regulatory proteins i.e. insulin
Nutrient and storage proteins i.e. ovalbumin
According to their solubility
Globular proteins: Soluble in Water
Fibrous proteins: Insoluble in water
WHY PROTEN AND PEPTIDE DRUGS?
The protein and peptide are very important in biological cells.
Lack of proteins and peptides causes diseases like Diabetes mellitus.
Diabetes mellitus is cause due to the lack of protein called INSULIN.
Now a day R-DNA technology and hybridoma also use in protein and peptide based pharmaceuticals.
FUNCTIONS
Transport and storage of small molecules.
Coordinated motion via muscle contraction.
Mechanical support from fibrous protein.
Generation and transmission of nerve impulses.
Enzymatic catalysis.
Immune protection through antibodies.
Control of growth and differentiation via hormones.
Problems with proteins
Elimination by B and T cells.
Proteolysis by endo/exo peptidases.
Small proteins filtered out by the kidneys very quickly.
Unwanted allergic reactions may develop (even toxicity).
Loss due to insolubility/adsorption.
"Bacterial metabolism: Fueling life's processes in tiny powerhouses."
Use of bacterial metabolism in biotechnology, biofuels, and other industries
Examples of how bacterial metabolism is harnessed for beneficial purposes
"Metabolism: the sum of chemical reactions in an organism, supporting growth, energy production, and vital functions."
"Bacterial Metabolism and Life: Pervading every aspect of life, shaping ecosystems, and influencing our world."
Bacterial metabolism refers to the collective chemical reactions and processes that occur within bacterial cells, enabling them to maintain life, grow, and reproduce. These metabolic activities involve a complex network of biochemical pathways that facilitate the conversion of nutrients into energy, biomolecules, and essential compounds necessary for bacterial survival.
Metabolic processes in bacteria include catabolic pathways that break down complex molecules (such as sugars) to release energy and anabolic pathways that build complex molecules (such as proteins, nucleic acids) using energy. Bacteria utilize various metabolic strategies based on their energy and carbon sources, including aerobic and anaerobic respiration, fermentation, and photosynthesis in photosynthetic bacteria.
The primary goals of bacterial metabolism are to obtain energy, synthesize necessary cellular components, regulate chemical processes, and adapt to changing environmental conditions. The understanding of bacterial metabolism is crucial for various fields, including medicine, agriculture, biotechnology, and environmental science, as it allows us to develop strategies to combat harmful bacteria, harness their metabolic capabilities for beneficial applications, and study their role in ecological systems.
Safalta Digital marketing institute in Noida, provide complete applications that encompass a huge range of virtual advertising and marketing additives, which includes search engine optimization, virtual communication advertising, pay-per-click on marketing, content material advertising, internet analytics, and greater. These university courses are designed for students who possess a comprehensive understanding of virtual marketing strategies and attributes.Safalta Digital Marketing Institute in Noida is a first choice for young individuals or students who are looking to start their careers in the field of digital advertising. The institute gives specialized courses designed and certification.
for beginners, providing thorough training in areas such as SEO, digital communication marketing, and PPC training in Noida. After finishing the program, students receive the certifications recognised by top different universitie, setting a strong foundation for a successful career in digital marketing.
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2. Proteins
• Proteins are macromolecules made up of amino
acids linked together in a specific sequence.
• They have diverse functions in cells, serving as
enzymes, structural components, transporters,
receptors, and more.
• The primary structure of a protein is its amino
acid sequence, and the secondary, tertiary, and
quaternary structures contribute to its three-
dimensional shape.
3. Proteins => Targets
• Nearly ALL therapeutic compounds,
manufactured or natural, exert their effects by
interacting with one or another form of
protein…
Enzymes Receptors Channels
Transporters Antigens
3
4. Protein Basics - 1
• 1 Gene 1 protein
• Translation polypeptide
• Maturation / Modification protein
4
Proteins are fundamental biological molecules that play a crucial role in various
cellular functions. To understand proteins better, you need to be familiar with
concepts such as genes, translocation, and modification:
5. Genes
• Genes are segments of DNA (or RNA in some
viruses) that carry the genetic information
needed to make proteins and perform various
other functions.
• Genes serve as templates for protein synthesis,
and the information within a gene determines
the sequence of amino acids in a protein.
• Genetic information is transcribed from DNA into
messenger RNA (mRNA), which serves as a
template for protein synthesis.
6. Translocation
• Here are a few key aspects of translocation in the context of nutrition:
• Nutrient Absorption: Translocation plays a crucial role in the absorption of nutrients from the digestive
system into the bloodstream. After digestion, nutrients such as glucose, amino acids, and fatty acids need
to be translocated across the intestinal epithelium to enter the bloodstream. Specialized transporters and
channels facilitate this process.
• Glucose Translocation: Glucose uptake into cells, particularly in muscle and fat tissue, is another important
example of translocation. This process is primarily mediated by glucose transporters, such as GLUT4, which
translocate from intracellular vesicles to the cell membrane in response to insulin or other signaling
molecules.
• Fatty Acid Transport: Fatty acids are translocated into cells for energy production or storage. This process
involves fatty acid transport proteins that facilitate the movement of fatty acids across cell membranes.
• Amino Acid Transport: Amino acids are essential for protein synthesis and other metabolic processes.
Translocation of amino acids into cells is vital for protein production and overall cellular function.
• Micronutrient Transport: Translocation also plays a role in the movement of vitamins and minerals across
cell membranes to support various biochemical reactions and metabolic processes.
• Hormone Action: Translocation can also refer to the movement of hormones or hormone receptors within
cells. For example, insulin signaling involves the translocation of GLUT4 transporters to the cell membrane,
enabling glucose uptake.
7. Translocation
Translocation in biochemistry for nutrition
students refers to the movement of nutrients,
molecules, and specific transporters across cell
membranes or within the body to support
essential metabolic processes. Understanding
these translocation mechanisms is fundamental
to comprehending how nutrients are absorbed
and utilized in the body and how metabolic
functions are regulated in response to
nutritional intake.
8. Protein Modification
• Proteins undergo various post-translational
modifications (PTMs) after their synthesis from mRNA.
These modifications can affect a protein's structure,
stability, and function.
• Common protein modifications include
phosphorylation (the addition of a phosphate group),
glycosylation (the addition of sugar moieties),
acetylation, methylation, and ubiquitination.
• Protein modifications can influence a protein's activity,
localization, and interactions with other molecules.
9. In summary …
Genes contain the genetic information required for
protein synthesis, and translocation can impact the
structure and function of proteins by altering the
genetic code. Once a protein is synthesized, it can
undergo various modifications that further
influence its function within the cell.
Understanding these concepts is crucial for
comprehending how genetic information is
translated into functional proteins and how
protein function can be regulated in cells.
10. Protein Basics – 2a
• Maturation / Modification protein
– Folding (1o -> 2o -> 3o agg -> 4o)
• Largely spontaneous
– Hydrophobic/hydrophilic interactions
– H-bonding
– R-group ionic interactions
– Modification of in-chain A.A.’s
– Cleavage
– Addition of non-protein groups
• Glycosylation, acylation, phosphorylation, etc.
10
11. Protein maturation and modification
Protein maturation and modification are
essential processes that occur after a protein is
synthesized. These processes help ensure that
proteins are properly functional and can carry
out their roles within the cell. Here's a brief
overview of protein maturation and
modification:
12. Protein Maturation
• Protein maturation involves the steps that a newly
synthesized protein goes through to attain its final,
functional conformation. It ensures that the protein
is properly folded and assembled into its active
form.
• Chaperone proteins, such as chaperonins or
chaperone molecules like heat shock proteins
(HSPs), assist in the correct folding of proteins.
• In some cases, proteins may require assistance from
other molecules or subunits to form functional
complexes. For example, hemoglobin, a protein that
carries oxygen in red blood cells, is composed of
multiple subunits that need to come together to
form the functional protein.
• Incorrectly folded or misfolded proteins can be
targeted for degradation to maintain cellular
integrity.
hemoglobin
13. Post-Translational Modifications (PTMs)
• Post-translational modifications are chemical alterations that occur after a protein
is synthesized. These modifications can profoundly impact a protein's function,
stability, localization, and interactions with other molecules.
• Common PTMs include:
– Phosphorylation: Addition of phosphate groups by protein kinases, often used
to regulate protein activity.
– Glycosylation: Addition of sugar moieties, which can affect protein stability
and function.
– Acetylation: Addition of acetyl groups, influencing protein localization and
activity.
– Methylation: Addition of methyl groups, which can regulate gene expression
and protein function.
– Ubiquitination: Attachment of ubiquitin molecules, targeting proteins for
degradation by the proteasome, (cellular signaling, and regulation of protein
activity).
– Sumoylation: Attachment of small ubiquitin-like modifiers (SUMO) to regulate
various cellular processes.
– PTMs can also affect protein-protein interactions, cellular signaling pathways,
14. Combination of protein maturation
and post-translational modifications
The combination of proper protein maturation
and post-translational modifications ensures
that proteins are correctly folded, localized, and
functional within the cell. These processes are
vital for the regulation of various cellular
functions and are crucial for the overall health
and homeostasis of an organism.
15. Protein Basics – 2b
• Sorting / Transport / Insertion
• Activation / Inactivation
• Degradation
• Structure determines function
15
Understanding the basics of proteins and their roles in sorting, transport, insertion,
activation, inactivation, degradation, and how structure determines function is
fundamental in the field of molecular biology and biochemistry. Here's an overview
of these concepts:
16. Sorting / Transport / Insertion:
• Sorting: Proteins can be sorted within cells to reach their
correct cellular locations. Signal sequences or motifs help
guide proteins to their destinations, such as the
endoplasmic reticulum, Golgi apparatus, or lysosomes.
• Transport: Once sorted, proteins can be transported within
the cell by vesicles or other mechanisms. For example, the
endoplasmic reticulum-to-Golgi transport relies on
vesicular trafficking.
• Insertion: Some proteins, such as transmembrane proteins,
need to be inserted into cellular membranes. This is often
mediated by hydrophobic regions that anchor the protein
in the lipid bilayer.
17. Activation / Inactivation / Degradation
• Activation: Proteins can be activated to perform their functions. For enzymes,
activation often involves a conformational change or the addition of cofactors or
coenzymes. For example, zymogens are inactive enzyme precursors activated by
proteolytic cleavage.
• Inactivation: Inactivation mechanisms exist to regulate protein function. This can
include reversible or irreversible modifications like phosphorylation,
dephosphorylation, or proteolytic cleavage.
• Degradation: Proteins have a finite lifetime and can be degraded when they are no
longer needed or when they become damaged. Two major protein degradation
pathways are the ubiquitin-proteasome system, which degrades specific proteins,
and lysosomal degradation, which processes cellular waste and engulfed material.
18. Ubiquitination
• Ubiquitination is a post-translational modification (PTM) of
proteins that plays a crucial role in regulating various
cellular processes, including protein degradation, signal
transduction, and the control of protein stability. The
process of ubiquitination involves the covalent attachment
of a small protein called ubiquitin to a target protein. This
modification is reversible and highly regulated, with
enzymes that add (ubiquitin ligases) and remove
(deubiquitinases) ubiquitin from target proteins.
• Ubiquitinationtags proteins for proteasomal degradation,
while autophagy is responsible for the degradation of
organelles and cytoplasmic components.
19. Structure Determines Function
• The three-dimensional structure of a protein is
critical to its function. Proteins have specific
active sites, binding sites, and functional domains
that interact with other molecules or substrates.
• A change in a protein's structure can lead to a
loss of function. For example, denaturation,
where a protein's native structure is disrupted,
can render it non-functional.
• Mutations in a protein's amino acid sequence can
also alter its structure, potentially leading to
dysfunctional or disease-causing proteins.
20. In summary …
In summary, proteins play vital roles in various
cellular processes, and their proper sorting,
transport, activation, inactivation, and
degradation are essential for maintaining
cellular functions and homeostasis*.
Additionally, a protein's structure is intimately
tied to its function, with even small changes in
structure potentially having significant
functional consequences.
*It encompasses the synthesis, folding, modification, trafficking, and degradation of proteins
to ensure that they function correctly and do not accumulate in harmful forms
21. What is Protein Biochemistry ?
-- After the molecular biology --
• Expression / Synthesis / PTranslM / Sort & Transport
/ Activate or Inactivate / Degrade
• Structure / Function
• Methods
• Identify / isolate / purify / modify
• Characterize
21
22. Protein biochemistry
Protein biochemistry is a branch of biochemistry that
focuses on the study of proteins, one of the most
important macromolecules in living organisms. It
encompasses the exploration of the structure, function,
synthesis, regulation, and interactions of proteins in
biological systems.
Protein biochemistry plays a critical role in advancing our
knowledge of how proteins work in the context of living
organisms. It is an interdisciplinary field that intersects
with genetics, molecular biology, cell biology, and
medicine, contributing to the development of new drugs,
treatments, and therapies for a wide range of diseases.
23. Why do Protein Biochemistry ?
A) Biotech. / Biopharm. / Manufacturing
• Product isolation
• Product purification
• Product modification
• Product characterization
• Product stability / storage
23
24. Why do Protein Biochemistry ?
B) Research
• Product isolation
• Product purification
• Product modification
• Product characterization
• Product stability / storage
24
25. Methods for Identifying & Localizing
• Study mutants
• Ligand binding
• In situ hybridization
• Chimeric (tagged) proteins (made GFP famous)
25
26. Biology/Chemistry of Protein Structure
Primary
Secondary
Tertiary
Quaternary
Assembly
Folding
Packing
Interaction
S
T
R
U
C
T
U
R
E
P
R
O
C
E
S
S
27. Protein Assembly
• Occurs at the ribosome
• Involves dehydration
synthesis and polymerization
of amino acids (attached to
tRNA)
28. Primary Structure
• Linear
• Ordered
• 1 dimensional
• Sequence of amino acid
polymer
• By convention, written from
amino end to carboxyl end
• A perfectly linear amino acid
polymer is neither functional
nor energetically favorable
folding!
primary structure of human insulin
CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT
29. Protein Folding (organized)
• Tumbles towards conformations that
reduce E (this process is thermo-
dynamically favorable).
• Yields secondary structure.
• Occurs in the cytosol.
• Involves localized spatial interaction
among primary structure elements.
• May or may not involve chaperone
proteins.
30. Secondary Structure
• non-linear
• 3 dimensional
• localized to regions of an
amino acid chain
• formed and stabilized by
hydrogen bonding,
electrostatic and van der
Waals interactions
31. Tertiary Structure
• Non-linear
• 3 dimensional
• Global but restricted to the amino
acid polymer
• Formed and stabilized by
hydrogen bonding, covalent (e.g.
disulfide) bonding, hydrophobic
packing toward core and
hydrophilic exposure to solvent
• A globular amino acid polymer
folded and compacted is
somewhat functional (catalytic)
and energetically favorable
interaction!
32. Protein Interaction
• Occurs in the cytosol,
• Involves interaction among tertiary structure
• May be promoted by chaperones, membrane proteins, cytosolic and
extracellular elements as well as the proteins’ own propensities
• ΔE (the change in energy) decreases further due to further desolvation
and reduction of surface area
• Globular proteins, e.g. hemoglobin, largely involved in catalytic roles
• Fibrous proteins, e.g. collagen, largely involved in structural roles
• Yields quaternary structure