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
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4. Protein Basics - 1
• 1 Gene 1 protein
• Translation polypeptide
• Maturation / Modification protein
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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.
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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
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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
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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
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24. Why do Protein Biochemistry ?
B) Research
• Product isolation
• Product purification
• Product modification
• Product characterization
• Product stability / storage
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25. Methods for Identifying & Localizing
• Study mutants
• Ligand binding
• In situ hybridization
• Chimeric (tagged) proteins (made GFP famous)
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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
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C
E
S
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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
