Praktikum Biokima Farmasi : Analisis Struktur Protein

Adam Hermawan

6 Mar 202212:07

Summary

TLDRThis video script delves into the intricate world of protein structure analysis in biochemistry labs. It explains the classification of proteins based on the number of amino acids, the four levels of protein structure (primary, secondary, tertiary, and quaternary), and the impact of a single amino acid change on diseases like sickle cell anemia. The script also covers the importance of hydrogen bonds in secondary structure and introduces the use of informatics in protein analysis, including databases like MCPE and Sanger. The practical session involves analyzing a specific protein, identifying its structure levels, and exploring its isoelectric point and scientific articles related to its function and diseases.

Takeaways

😀 The video script discusses the final topic of the biochemistry lab, which is the structure analysis of proteins.
🔍 Proteins are composed of amino acid chains and are classified based on the number of amino acids present in the chain, such as peptides, dipeptides, tripeptides, and polypeptides.
🧬 Proteins generally consist of 100-10,000 amino acids linked together and are the building blocks of life.
🌐 There are four levels of protein structure: primary (linear sequence of amino acids), secondary (shape based on peptide chain folding like alpha helix), tertiary (3D shape of the folded polypeptide chain), and quaternary (arrangement of multiple polypeptide chains).
🔬 The script highlights the importance of the primary structure, where even a single amino acid change can significantly affect the protein's function and lead to diseases like sickle cell anemia.
🔑 Secondary structures are stabilized by hydrogen bonds, with alpha helix and beta sheets being common examples.
🤝 Tertiary structure involves various interactions such as hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions that give the protein its 3D shape.
🌟 Quaternary structure refers to proteins made up of multiple polypeptide chains or subunits that together perform a specific function.
📚 The script introduces the use of bioinformatics to analyze protein structures using molecular information related to DNA, RNA, and amino acids, facilitated by software and databases.
💻 The lab session involves working with a specific protein code, using methodologies outlined in lab manuals and video tutorials, and analyzing the protein's structure and isoelectric point.
📝 Participants are expected to document their findings, explain the significance of the protein's structure, and research its relation to diseases or other targets.

Q & A

What is the basic unit of a protein?
-The basic unit of a protein is the amino acid, which is composed of carbon, hydrogen, oxygen, and nitrogen.
How are proteins classified based on the number of amino acids?
-Proteins are classified based on the number of amino acids they contain: peptides with less than 50 amino acids, dipeptides with two amino acids, tripeptides with three amino acids, and polypeptides with more than 10 amino acids. Proteins generally consist of 100-10,000 amino acids.
What are the four levels of protein structure?
-The four levels of protein structure are primary (linear sequence of amino acids), secondary (local folding patterns like alpha-helix and beta-sheet), tertiary (three-dimensional structure of the polypeptide chain), and quaternary (arrangement of multiple polypeptide chains).
What is the significance of the primary structure of a protein?
-The primary structure, which is the sequence of amino acids, is crucial as even a single amino acid change can significantly alter the protein's secondary, tertiary, and quaternary structures, affecting its function.
How does a change in a single amino acid affect a protein?
-A change in a single amino acid can alter the protein's conformation, potentially disrupting its secondary and tertiary structures, and consequently, its function, as seen in diseases like sickle cell anemia.
What stabilizes the secondary structure of proteins?
-The secondary structure of proteins is stabilized by hydrogen bonds, which form between the backbone atoms of the polypeptide chain.
What are the types of interactions that contribute to the tertiary structure of a protein?
-The tertiary structure of a protein is stabilized by various interactions including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
What is the quaternary structure of a protein?
-The quaternary structure refers to the arrangement of multiple polypeptide chains or subunits, which together form a functional multi-subunit protein complex.
Why is the study of protein structure important in understanding diseases?
-Studying protein structure is important in understanding diseases because abnormalities in protein structure can lead to various conditions, such as sickle cell anemia, where a single amino acid change in hemoglobin alters its shape and function.
How can computational approaches aid in protein structure analysis?
-Computational approaches, such as bioinformatics, involve the use of software and databases to analyze molecular data related to DNA, RNA, and proteins, facilitating the understanding of protein structure and function.
What is the purpose of the practical exercise mentioned in the script?
-The practical exercise aims to explore protein structures using computational methods, where students will analyze a specific protein code, determine its secondary and tertiary structures, and understand its isoelectric point using databases like ExPASy.

Outlines

00:00

🧬 Protein Structure Analysis

This paragraph introduces the final topic of the biochemistry lab, which is protein structure analysis. Proteins are composed of amino acid chains and are classified based on the number of amino acids they contain. Peptides have less than 50 amino acids, while polypeptides have more than 10 but less than 50, and proteins generally consist of 100-10,000 amino acids. The paragraph discusses the four levels of protein structure: primary (the sequence of amino acids), secondary (the conformation of the peptide chain, such as alpha helix and beta sheets), tertiary (the three-dimensional structure of the folded polypeptide chain), and quaternary (the arrangement of multiple polypeptide chains into a multi-subunit structure). The paragraph also touches on the importance of the primary structure in determining the overall protein structure and function, and how a single amino acid difference can lead to significant changes in protein structure and function, as seen in diseases like sickle cell anemia.

05:01

🔬 Impact of Amino Acid Changes on Protein Structure

This paragraph delves into how a single amino acid substitution can drastically alter protein structure and function. It uses the example of sickle cell anemia, where a change from glutamic acid to valine at the sixth position results in a different protein conformation. This alteration affects the secondary, tertiary, and quaternary structures of the protein, leading to the characteristic sickle shape of red blood cells in the disease. The paragraph also discusses the stabilizing forces of secondary structures, such as hydrogen bonds, and how different amino acid properties (polar vs. nonpolar) can influence these interactions. It further explains the various interactions present in tertiary structures, including hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions. The paragraph concludes with an introduction to the concept of quaternary structure, which involves multiple polypeptide chains forming a functional protein complex.

10:04

💻 Bioinformatics Approach to Protein Structure Analysis

The final paragraph shifts the focus to the application of bioinformatics in studying protein structures. It mentions that bioinformatics involves the use of software and databases to analyze molecular information related to DNA, RNA, proteins, and amino acids. The paragraph outlines the activities for a lab session where students will be divided into groups to analyze a specific protein using the MCPE database. Students will follow a methodological approach as instructed in the lab manual and video tutorials. The lab work involves taking screenshots at each step, explaining the significance of the protein's primary, secondary, and tertiary structures, and determining the isoelectric point using the Exoelectric database. Additionally, students are tasked with finding a scientific article related to the analyzed protein and its connection to diseases or therapeutic targets.

Mindmap

Keywords

💡Protein Structure Analysis

Protein Structure Analysis is the process of determining the three-dimensional arrangement of atoms within a protein molecule. It is central to the video's theme as it discusses the various levels of protein structure and their significance in biological functions. The script mentions the four levels of protein structure: primary, secondary, tertiary, and quaternary, which are essential for understanding how proteins fold and function in the body.

💡Amino Acids

Amino Acids are the building blocks of proteins, consisting of carbon, hydrogen, oxygen, and nitrogen. They are the core components discussed in the script, as they form the sequence that makes up the primary structure of a protein. The video emphasizes that even a single change in an amino acid can drastically affect the protein's structure and function, as seen in sickle cell anemia.

💡Peptides

Peptides are short chains of amino acids linked by peptide bonds. The script differentiates between different lengths of peptides, such as dipeptides (two amino acids), tripeptides (three amino acids), and polypeptides (more than ten amino acids). This distinction is important for understanding the progression from simple peptide chains to complex protein structures.

💡Primary Structure

The Primary Structure refers to the linear sequence of amino acids in a protein, which is determined by the genetic code. In the script, it is mentioned that this sequence starts from the N-terminal and ends at the C-terminal, and a change in even one amino acid can significantly alter the protein's properties, as exemplified by sickle cell anemia.

💡Secondary Structure

Secondary Structure describes the local folding of the protein's primary structure into regular patterns such as alpha-helices and beta-sheets, which are stabilized by hydrogen bonds. The script explains that these structures are crucial for the protein's overall shape and stability, and they are formed based on the peptide bond's ability to rotate and form hydrogen bonds.

💡Tertiary Structure

Tertiary Structure is the overall three-dimensional shape of a single polypeptide chain, resulting from more complex interactions such as hydrogen bonds, ionic bonds, and hydrophobic interactions. The script illustrates this with examples of how different secondary structures come together to form the complete folded protein, which is essential for its function.

💡Quaternary Structure

Quaternary Structure refers to the assembly of multiple polypeptide subunits or subunits to form a functional protein complex. The script mentions that proteins like hemoglobin have a quaternary structure, which is composed of multiple subunits that work together to perform specific biological functions.

💡Isoelectric Point

The Isoelectric Point (pI) is the pH at which a particular molecule carries no net electrical charge. In the context of the video, determining the isoelectric point is part of the protein analysis process, which can be found using databases like ExPASy, as mentioned in the script.

💡Molecular Informatics

Molecular Informatics is the application of computational methods to analyze molecular data, such as DNA, RNA, and proteins. The script introduces this concept as a way to facilitate the study of protein structures and their relationships with diseases or other biological targets using databases and software tools.

💡Sickle Cell Anemia

Sickle Cell Anemia is a genetic disorder that affects the structure of hemoglobin, causing red blood cells to become misshapen and break down more rapidly. The script uses this disease as an example to illustrate how a single amino acid substitution in the protein's primary structure can lead to significant changes in the protein's function and overall health implications.

💡Hydrogen Bonds

Hydrogen Bonds are a type of chemical bond that plays a crucial role in stabilizing the secondary structure of proteins. The script explains that these bonds are formed between the peptide backbone's atoms and are essential for maintaining the alpha-helix and beta-sheet conformations within a protein.

Highlights

Introduction to the final topic of biochemistry lab practice, protein structure analysis.

Proteins are composed of amino acid chains and classified based on the number of amino acids present.

Peptides are categorized into dipeptides, tripeptides, and polypeptides based on the number of amino acids.

Proteins generally consist of 100-10,000 amino acids linked together.

Amino acids are composed of atoms like carbon, hydrogen, oxygen, and nitrogen.

There are four levels of protein structure: primary, secondary, tertiary, and quaternary.

Primary structure refers to the sequence of amino acids in a protein.

Secondary structure includes conformations such as alpha helix and beta sheets stabilized by hydrogen bonds.

Tertiary structure is the three-dimensional shape of the polypeptide chain.

Quaternary structure describes the arrangement of multiple polypeptide chains into a multi-subunit structure.

A single amino acid change can significantly alter a protein's structure and function, as seen in sickle cell anemia.

The importance of hydrogen bonds in stabilizing secondary structures like alpha helix and beta sheets.

Examples of secondary structures in lysozyme and their stabilization mechanisms.

Tertiary structure involves various interactions including hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions.

Quaternary structure's role in the function of multi-subunit proteins, such as hemoglobin.

The use of computational approaches in protein structure analysis, involving molecular information from DNA, RNA, and amino acids.

Introduction to databases commonly used in pharmaceutical studies, such as MCPE and Sanger.

Practical lab exercise involving analysis of a specific protein using computational methods and databases.

Students will be divided into groups to analyze a protein with a given code, following methods outlined in the lab manual and video tutorials.

Students are expected to explain the secondary, tertiary, and quaternary structures of the proteins they analyze.

Identifying the isoelectric point of proteins using databases like Exo.

Researching scientific articles related to the analyzed protein and its connection to diseases or targets.