Primary structure of protein
Secondary structure of protein
Tertiary structure of protein
Quaternary structure of protein
Methods to determine protein structure
Conclusion
References
METHODS TO DETERMINE PROTEIN STRUCTURE
Each protein has a unique sequence of amino acids.
The amino acids are held together in a protein by
covalent peptide bonds or linkages.
A peptide bond are formed when amino group of an
amino acid combines with the carboxyl group of another.
The conformation of polypeptide chain by twisting or folding is referred to as secondary structure.
Two types of secondary structures α-helix and β-sheet are mainly identified.
α-Helical structure was proposed by Pauling and Corey in 1951.
It occurs when the sequence of amino acids are linked by hydrogen bonds.
Each turn of α-helix contains 3.6 amino acids.
β-pleated sheets are composed of two or more segments of fully extended peptide chains.
β-Sheets may be arranged either in parallel or anti-parallel direction.
Many globular proteins contain combinations of α-helix and β-pleated sheet secondary structure, these patterns are called supersecondary structures also called motifs.
The three dimensional arrangement of protein structure is referred to as tertiary structure.
It is a compact structure with hydrophobic side chains held interior while the hydrophilic groups are on the surface.
This type of arrangement provide stability of the molecule.
Besides the H-bongs, disulfide bonds, ionic interactions, hydrophobic interactions also contribute to the tertiary structure.
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
Primary structure of protein
Secondary structure of protein
Tertiary structure of protein
Quaternary structure of protein
Methods to determine protein structure
Conclusion
References
METHODS TO DETERMINE PROTEIN STRUCTURE
Each protein has a unique sequence of amino acids.
The amino acids are held together in a protein by
covalent peptide bonds or linkages.
A peptide bond are formed when amino group of an
amino acid combines with the carboxyl group of another.
The conformation of polypeptide chain by twisting or folding is referred to as secondary structure.
Two types of secondary structures α-helix and β-sheet are mainly identified.
α-Helical structure was proposed by Pauling and Corey in 1951.
It occurs when the sequence of amino acids are linked by hydrogen bonds.
Each turn of α-helix contains 3.6 amino acids.
β-pleated sheets are composed of two or more segments of fully extended peptide chains.
β-Sheets may be arranged either in parallel or anti-parallel direction.
Many globular proteins contain combinations of α-helix and β-pleated sheet secondary structure, these patterns are called supersecondary structures also called motifs.
The three dimensional arrangement of protein structure is referred to as tertiary structure.
It is a compact structure with hydrophobic side chains held interior while the hydrophilic groups are on the surface.
This type of arrangement provide stability of the molecule.
Besides the H-bongs, disulfide bonds, ionic interactions, hydrophobic interactions also contribute to the tertiary structure.
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
A powerpoint presentation made for an international geometry lesson during a Comenius visit in Gimnazjum 17 in Wrocław within the project 'Culture Beyond Borders'
Protein is essential for building and repairing tissues, producing enzymes and hormones, and maintaining overall health. Good sources include meat, poultry, fish, eggs, dairy, legumes, nuts, and seeds. How can I assist you further with protein
Proteins can be classified based on various criteria, including their structure, function, and source. Structurally, proteins are categorized into four primary levels:
1. Primary structure: The sequence of amino acids in a protein chain.
2. Secondary structure: Local folding patterns such as alpha helices and beta sheets.
3. Tertiary structure: The overall 3D shape of the protein molecule.
4. Quaternary structure: The arrangement of multiple protein subunits, if applicable.
Functionally, proteins can be classified based on their roles in the body, such as enzymes, structural proteins, hormones, antibodies, transport proteins, and more.
Finally, proteins can also be classified based on their source, such as animal proteins (found in meat, dairy, eggs) and plant proteins (found in legumes, nuts, seeds). Let me know if you need more details on any specific classification!
Proteins play crucial roles in the body, serving as building blocks for tissues, enzymes for biochemical reactions, hormones for signaling, antibodies for immune defense, and transporters for molecules across cell membranes. Without adequate protein intake, various physiological functions would be impaired, leading to health issues. Thus, ensuring sufficient protein intake is essential for overall health and well-being.
Protein is an essential macronutrient in our diet, crucial for building and repairing tissues, supporting immune function, and regulating various processes in the body. In terms of nutrition, it's important to consume an adequate amount of protein daily, with recommendations varying based on factors like age, sex, weight, activity level, and overall health status.
For most adults, the recommended dietary allowance (RDA) for protein is around 0.8 grams per kilogram of body weight per day. However, individual protein needs may vary, and some individuals, such as athletes or those recovering from injury, may require higher protein intake.
It's also essential to consume a variety of protein sources to ensure you get all the essential amino acids your body needs. Good sources of protein include lean meats, poultry, fish, eggs, dairy products, legumes, nuts, seeds, and tofu.
Incorporating protein-rich foods into meals and snacks throughout the day can help maintain muscle mass, support satiety, and contribute to overall nutritional balance. If you have specific dietary goals or health concerns, consulting with a registered dietitian or nutritionist can help tailor your protein intake to meet your individual needs.
Dietary sources of protein include a wide range of foods, both from animal and plant sources. Here are some common examples:
1. **Animal Sources**:
- Meat: Beef, pork, lamb, veal, etc.
- Poultry: Chicken, tur
Protein - a macromolecule is explained. The general characteristics, its chemical and structural components are described. Protein sources, nutritive value also dealt in it. As a major portion classification of proteins are given. Along with it properties, both physical and chemical properties and the various functions of proteins are also given
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer.
Amino acisd structure
Peptide bond formation
Analysis of protein Structure- X-ray Crystallography
Different structural levels of proteins with examples.
Importance of protein structure
Creutzfeldt-Jacob-Disease due to changes in normal protein conformation.
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
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All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
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💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
2. DEFINITIONS OF PROTEIN
• Proteins are one of the essential
building blocks of the human body.
• They provide amino acids, which are a nutritional
requirement of the body to produce its own proteins
and a variety of nitrogen-based molecules.
• It is common for programs to recommend a minimum
of 50 grams of protein per day to maintain healthy
levels.
• Proteins vary in structure as well as function. They are
constructed from a set of 20 amino acids and have
distinct three-dimensional shapes.
3. General Characteristics of Proteins
• They are the most complex and most diverse in chemical composition,
conferring upon the different tissues.
• Protein molecule contains elements of C, H, O,N, S, and P together with
traces of Fe, Cu, I, Mn, and Zn.
• It has a molecular weight of 5,000 to 3,000,000
• They are the most important of the biologic substances being the
fundamental constituent of cell cytoplasm.
• They supply not only heat and energy but also material for building and
repair.
• Unlike carbohydrates and lipids, only small amounts of protein is
temporarily stored in the body, and which can be quickly used up upon
demand.
5. FUNCTIONS OF PROTEIN
• Antibodies - are specialized proteins involved in defending the
body from antigens (foreign invaders). One way antibodies destroy
antigens is by immobilizing them so that they can be destroyed by
white blood cells.
• Enzymes - are proteins that facilitate biochemical reactions. They
are often referred to as catalysts because they speed up chemical
reactions. Examples include the enzymes lactase and pepsin.
Lactase breaks down the sugar lactose found in milk. Pepsin is a
digestive enzyme that works in the stomach to break down
proteins in food.
• Hormonal Proteins - are messenger proteins which help to
coordinate certain bodily activities. Examples include insulin,
Insulin regulates glucose metabolism by controlling the bloodsugar concentration.
6. FUNCTIONS OF PROTEIN
• Contractile Proteins - are responsible for movement. Examples include
actin and myosin. These proteins are involved in muscle contraction
and movement.
• Structural Proteins - are fibrous and stringy and provide support.
Examples include keratin, collagen, and elastin. Keratins strengthen
protective coverings such as hair, quills, feathers, horns, and beaks.
Collagens and elastin provide support for connective tissues such as
tendons and ligaments.
• Storage Proteins - store amino acids. Examples include ovalbumin and
casein. Ovalbumin is found in egg whites and casein is a milk-based
protein.
• Transport Proteins - are carrier proteins which move molecules from
one place to another around the body. Examples include hemoglobin
and cytochromes. Hemoglobin transports oxygen through the blood.
Cytochromes operate in the electron transport chain as electron carrier
proteins.
7. Classification of Proteins
Based on Composition:
• Simple proteins – composed of entirely amino acids
only.
Ex. Albumin, Globulin
• Complex or Conjugated proteins – made up of
amino acids and other organic compounds. The nonamino acid group is termed as the prosthetic group.
Ex. Nucleoproteins, lipoproteins,
glycoproteins, metalloproteins
8. Classification of Proteins
Based on Axial Ratio:
Axial ratio is the ratio of the length to the breath.
• Globular proteins – with axial ratio less than 10 but
not below 3 or 4. They are compactly folded and
coiled.
Ex. Insulin, plasma albumin, globulin,
enzymes
• Fibrous proteins – with axial ratio greater than 10.
They are spiral and helical and are cross linked by
disulfide and hydrogen bonds.
Ex. Keratin, myosin, elastin, collagen
9. Globular Proteins
• Globular proteins have
their axial ratio less
than 10 but not below 3
or 4. They are
compactly folded and
coiled.
• Examples are insulin,
plasma albumin,
globulin, enzymes
10. Fibrous Proteins
• Fibrous proteins are
spiral and helical
and are cross linked
by disulfide and
hydrogen bonds
• Examples are
keratin, myosin,
elastin, collagen
12. Shape = Amino Acid Sequence
• Proteins are made of 20 amino acids linked
by peptide bonds
• Polypeptide backbone is the repeating
sequence of the N-C-C-N-C-C… in the
peptide bond
• The side chain or R group is not part of the
backbone or the peptide bond
15. Different Amino Acid Classes
H2N
H
O
C
C
C
H
H2N
OH
Generic
H
H
Non-polar
H
O
C
O
C
C
C
Acid OH
H
O
Amine
H2N
Aspartic
acid
H2N
H
OH
?R
C
C
HS
C
Polar
Acid
C
Cysteine
C
O
Alanine
OH
H
H
OH
O
H
H2N
H
H
Basic
C
C
H+N
C
C
C
H
NH
C
Histidine
OH
H
16. Non-Polar
Amino Acids
Glycine O
H2N
C
C
OH
Valine O
H
H
H2N
H
H
C
C
OH
H
C
C
C
H
H
CH3
OH
H
H2N
CH3
H
H3C
C
C
C
H
C
H
H
C
H
O
Isoleucine
H3C
H
OH
H
C
C
OH
H
H
C
C
C
C
H3C
H
PhenylalanineO
H2N
H2N
H
H
C
H3C
H
C
H
C
OH
C
H2N
Leucine O
C
H2N
Alanine O
MethionineO
OH
H
H3C
TryptophanO
H2N
H
H
S
C
C
C
H
NH
H2C
H2C
OH
H
Proline O
H2N+
C
C
CH2
H
Protein Structure
OH
17. Polar Amino Acids
Serine O
H2N
H
C
C
C
H2N
OH
H
H
H
CH3
HO
Cysteine O
H
HS
C
C
C
H
C
C
C
H2N
H
H
O
OH
H
H
C
C
OH
H
C
H
H
Asparagine O
OH
H2N
OH
C
H
H2N
Tyrosine O
Threonine O
C
C
C
C
H
NH2
Glutamine O
HO
H2N
OH
H
H
H
O
H
H
NH2
C
C
C
C
C
H
OH
19. Basic Amino Acids
Histidine O
H2N
H
C
C
H+N
C
C
C
H2N
H
H
H
NH
C
Lysine O
OH
H
H
H
C
+H N
3
C
C
C
C
OH
Arginine O
H
H2N
H
C
H
H
H
H
H
H
+H N
2
N
C
C
C
C
C
OH
H
H
C
H
H
H
NH2
Protein Structure
20. Levels of Protein Organization
• Primary Structure - The sequence of amino
acids in the polypeptide chain
• Secondary Structure - The formation of
helices and b pleated sheets due to hydrogen
bonding between the peptide backbone
• Tertiary Structure - Folding of helices and
sheets influenced by R group bonding
• Quaternary Structure - The association of more
than one polypeptide into a protein complex
influenced by R group bonding
21. Levels of Protein Organization
Primary Structure
Met-Gly-Ala-Pro-His-Ile-Asp-Glu-Met-Ser-Thr-..
The sequence of amino acids in the primary structure determines the folding
of the molecule.
Protein Structure
22. Protein Secondary Structure
• The peptide backbone has areas of positive
charge and negative charge
• These areas can interact with one another to
form hydrogen bonds
• The result of these hydrogen bonds are two
types of structures:
helices
b pleated sheets
24. H
N
Protein Secondary Structure:
H
C
Helix
C
N
O
H
C
C
O
N
H
- +
C
H O
H O
C
N
O
C
C
O
H
N
H
N
C
O
H
C
O
C
C
C
O
H
N
H
H
N
C
C
C
N
H
H
C
H HO
C
H
C
H
OH
25. Protein Secondary Structure:
Helix
R groups stick
out from the
helix influencing
higher levels of
protein
organization
R
R
R
R
R
R
R
R
R
R
R
R
R
R
26. M
L
L
S
R
Q
S
I
R
F
T
L
F
K
A
R
C
Y
P
P
S
L
The order of the amino acids
determines the hydrogen
bonding
Neutral Non-polar
Polar
Basic
Acidic
MLSLRQSIRFFKPATRTLCSSRYLL
T
S
R
Yeast Cytochrome C Oxidase
Subunit IV Leader
• This would localise specific classes of
amino acids in specific parts of the helix
27. Protein Secondary Structure:
b Pleated Sheet
C
O
C
H
C N
N
H
O
C
N
H
C
C
O
C
C
O
H
N
C
O
C
H
C N
N
H
O
C
N
H
C
C
O
C
C
O
H
N
C
O
C
H
C N
N
H
O
C
N
H
C
C
O
C
C
O
H
N
C
O
C
H
C N
N
H
O
C
N
H
C
C
O
C
O
H
N
C
28. Protein Secondary Structure:
b Pleated Sheet
C
O
C
N
H
O
C
C
H
C N
N
H
O
C
N
H
C
C
O
C
O
H
N
H
C N
C
C
O
O
C
N
H
O
C
C
C
H
C N
N
H
O
C
N
H
C
C
O
C
O
H
N
H
C N
C
C
O
O
C
N
H
O
C
C
C
H
C N
N
H
O
C
N
H
C
C
O
C
O
H
N
H
C N
C
C
O
O
C
N
H
O
C
C
C
H
C N
N
H
O
C
N
H
C
C
O
C
O
H
N
H
C N
C
O
C
29. Levels of Protein Organization
Tertiary Structure
• Tertiary structure results from the folding
of helices and b pleated sheets
• Factors influencing tertiary structure
include:
• Hydrophobic interactions
• Hydrogen bonding
• Disulphide bridges
• Ionic bonds
35. Levels of Protein Organization
Quaternary Structure
• Quaternary structure results from the interaction
of independent polypeptide chains
• Factors influencing quaternary structure include:
• Hydrophobic interactions
• Hydrogen bonding
• The shape and charge distribution on amino
acids of associating polypeptides
38. Globular
• e.g. haemoglobin
• 3º structure normally
folds up in a ball
• hydrophilic R groups
point outwards
• Hydrophobic R
groups point inwards
• soluble
• metabolic functions
and
Fibrous
• e.g. collagen
• 2º structure does not
fold up, form fibres
• not surrounded by
hydrophilic R groups
• insoluble
• structural functions
39. Haemoglobin
• Haemoglobin is a globular protein with
a prosthetic ‘iron’ group
• In adults, hemoglobin is made up of 4
polypeptides (2 polypeptide chains
and 2 b polypeptide chains)
• Each polypeptide surrounds a
prosthetic ‘haem’ group
• Hydrophobic interactions between side
groups pointing inwards maintain the
structure
• Hydrophilic side chains point outwards
making it soluble
b
Fe
b
42. Protein Folding
• The peptide bond allows for rotation
around it and therefore the protein can fold
and orient the R groups in favorable
positions
• Weak non-covalent interactions will hold
the protein in its functional shape – these
are weak and will take many to hold the
shape
44. Globular Proteins
• The side chains will help determine the
conformation in an aqueous solution
45. Hydrogen Bonds in Proteins
• H-bonds form between 1) atoms involved in the peptide bond;
2) peptide bond atoms and R groups; 3) R groups
46. Protein Folding
• Proteins shape is determined by the
sequence of the amino acids
• The final shape is called the conformation
and has the lowest free energy possible
• Denaturation is the process of unfolding
the protein
– Can be done with heat, pH or chemical
compounds
– The chemical compound can be removed and
have the protein renature or refold
47. Refolding
• Molecular chaperones are small proteins that help
guide the folding and can help keep the new
protein from associating with the wrong partner
48. Protein Folding
• 2 regular folding patterns
have been identified –
formed between the bonds
of the peptide backbone
• -helix – protein turns like a
spiral – fibrous proteins
(hair, nails, horns)
• b-sheet – protein folds back
on itself as in a ribbon –
globular protein
49. b Sheets
• Core of many proteins is the b
sheet
• Form rigid structures with the Hbond
• Can be of 2 types
– Anti-parallel – run in an
opposite direction of its
neighbor (A)
– Parallel – run in the same
direction with longer looping
sections between them (B)
50. Helix
• Formed by a H-bond between
every 4th peptide bond – C=O to
N-H
• The helix can either coil to the
right or the left
• Can also coil around each other –
coiled-coil shape – a framework
for structural proteins such as
nails and skin
52. Domains
• A domain is a basic structural unit of a
protein structure – distinct from those that
make up the conformations
• Part of protein that can fold into a stable
structure independently
• Different domains can impart different
functions to proteins
• Proteins can have one to many domains
depending on protein size
54. Useful Proteins
• There are thousands and thousands of different
combinations of amino acids that can make up
proteins and that would increase if each one had
multiple shapes
• Proteins usually have only one useful
conformation because otherwise it would not be
efficient use of the energy available to the system
• Natural selection has eliminated proteins that do
not perform a specific function in the cell
55. Protein
Families
• Have similarities in amino acid sequence and 3-D
structure
• Have similar functions such as breakdown
proteins but do it differently
56. Proteins – Multiple Peptides
• Non-covalent bonds can form interactions
between individual polypeptide chains
– Binding site – where proteins interact with one
another
– Subunit – each polypeptide chain of large
protein
– Dimer – protein made of 2 subunits
• Can be same subunit or different subunits
59. Protein Assemblies
• Proteins can form very
large assemblies
• Can form long chains if
the protein has 2 binding
sites – link together as a
helix or a ring
• Actin fibers in muscles
and cytoskeleton – is
made from thousands of
actin molecules as a
helical fiber
60. Types of Proteins
• Globular Proteins – most of what we have
dealt with so far
– Compact shape like a ball with irregular
surfaces
– Enzymes are globular
• Fibrous Proteins – usually span a long
distance in the cell
– 3-D structure is usually long and rod shaped
61. Important Fibrous Proteins
• Intermediate filaments of the cytoskeleton
– Structural scaffold inside the cell
• Keratin in hair, horns and nails
• Extracellular matrix
– Bind cells together to make tissues
– Secreted from cells and assemble in long fibers
• Collagen – fiber with a glycine every third amino
acid in the protein
• Elastin – unstructured fibers that gives tissue an
elastic characteristic
63. Stabilizing Cross-Links
• Cross linkages can be between 2 parts of a protein or
between 2 subunits
• Disulfide bonds (S-S) form between adjacent -SH
groups on the amino acid cysteine
64. Proteins at Work
• The conformation of a protein gives it a unique
function
• To work proteins must interact with other
molecules, usually 1 or a few molecules from the
thousands to 1 protein
• Ligand – the molecule that a protein can bind
• Binding site – part of the protein that interacts
with the ligand
– Consists of a cavity formed by a specific arrangement
of amino acids
66. Formation of Binding Site
• The binding site forms when amino acids from within
the protein come together in the folding
• The remaining sequences may play a role in regulating
the protein’s activity
67. Antibody Family
• A family of proteins that can be created to
bind to almost any molecule
• Antibodies (immunoglobulins) are made in
response to a foreign molecule ie. bacteria,
virus, pollen… called the antigen
• Bind together tightly and therefore
inactivates the antigen or marks it for
destruction
68. Antibodies
• Y-shaped molecules with 2 binding sites at
the upper ends of the Y
• The loops of polypeptides on the end of the
binding site are what imparts the
recognition of the antigen
• Changes in the sequence of the loops make
the antibody recognize different antigens specificity