PROTEIN FOLDING

Summary

This video explains how proteins are made up of polypeptide chains, composed of 20 different amino acids linked by peptide bonds. It outlines the four levels of protein structure: primary (amino acid sequence), secondary (hydrogen bonds forming alpha helixes and beta sheets), tertiary (3D folding based on polar and nonpolar amino acids), and quaternary (interacting polypeptide chains). The video also discusses protein folding mechanisms and introduces three classes of proteins: globular, fibrous, and membrane proteins. These shapes and solubility characteristics define their biological roles.

Takeaways

• 🧬 Proteins are made of folded polypeptide chains composed of 20 different amino acids, each with unique chemical properties.
• 🔗 Amino acids are linked by covalent peptide bonds, forming a repeating polypeptide backbone with distinct side chains.
• 🔄 Protein folding results in different conformations, which are the spatial arrangements of atoms without bond breakage.
• 📊 Protein structure is categorized into four levels: primary (amino acid sequence), secondary (hydrogen bonding interactions), tertiary (3D folding), and quaternary (multiple polypeptide chains).
• 🔁 Secondary structures include alpha helices and beta sheets, which are formed by hydrogen bonds between peptide bonds.
• 🌀 Alpha helices coil like springs, with hydrogen bonds between every 3.6 amino acids, giving the structure polarity with an N-terminus and C-terminus.
• 🧩 Beta sheets form parallel or antiparallel chains with hydrogen bonds between neighboring chains, contributing to the protein's overall structure.
• 🌊 Hydrophobic interactions drive protein folding, with nonpolar amino acids gathering inside the protein and polar amino acids forming bonds on the surface with water molecules.
• 📦 Tertiary structure forms as secondary structures interact, with nonpolar amino acids collapsing inward and long-range interactions shaping the final protein structure.
• 🔬 Proteins are classified into three categories: globular (spherical and soluble), fibrous (linear and insoluble), and membrane (associated with cell membranes).

Q & A

What are proteins made up of?

Proteins are made up of folded polypeptide chains composed of 20 different amino acids linked via covalent peptide bonds.

What is the polypeptide backbone?

The polypeptide backbone is the sequence of atoms repeating to form the peptide bonds in a polypeptide chain.

What makes each amino acid different from the others?

Each amino acid has a unique sidechain, which can be polar or nonpolar, giving it distinct chemical properties.

What are protein conformations?

Conformations are the spatial arrangements of atoms in a protein that result from movement without breaking bonds.

What are the four levels of protein structure?

Protein structure is described in four levels: primary (amino acid sequence), secondary (local interactions like alpha helices and beta sheets), tertiary (3D shape), and quaternary (multiple polypeptide subunits interacting).

How is secondary structure formed?

Secondary structure is formed by hydrogen bond interactions between adjacent amino acids, leading to structures like alpha helices and beta sheets.

What causes proteins to fold into their tertiary structure?

The pattern of polar and nonpolar amino acids in a polypeptide chain drives the folding process, with nonpolar amino acids aggregating to avoid water and polar amino acids interacting with the water environment.

What is the difference between parallel and anti-parallel beta sheets?

Parallel beta sheets are made from neighboring chains running in the same direction, while anti-parallel beta sheets are formed by chains running in opposite directions.

What is hydrophobic collapse during protein folding?

Hydrophobic collapse is the aggregation of nonpolar amino acids during the early stages of protein folding, reducing their interaction with water and promoting proper protein folding.

What are the three basic classes of proteins, and how do they differ?

The three basic classes are globular, fibrous, and membrane proteins. Globular proteins are spherical and water-soluble, fibrous proteins have linear structures and provide structural support, and membrane proteins are associated with cell membranes.

Outlines

00:00

🔬 Introduction to Protein Structure

Proteins are composed of folded polypeptide chains made up of 20 distinct amino acids, each with unique chemical properties. These amino acids are linked by covalent peptide bonds. The sequence of repeating atoms forming these peptide bonds is called the polypeptide backbone, and the side chains of the amino acids can be either polar or nonpolar. Protein structures can adopt various conformations without breaking bonds, and these structures are classified into four levels: primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence, which contains all the information needed for higher-order structures.

🔗 Secondary Structures: Alpha Helices and Beta Sheets

Secondary structures arise from hydrogen bonds between adjacent amino acids. These bonds form two main types of structures: alpha helices and beta pleated sheets. An alpha helix coils like a spring with one turn every 3.6 amino acids, where the NH group forms a hydrogen bond with the C=O group of another peptide one coil away. This gives the polypeptide chain polarity, with one end having a positive charge and the other a negative charge. Beta sheets, on the other hand, can be parallel or antiparallel, depending on the direction of neighboring chains. These sheets are stabilized by inter-strand hydrogen bonds.

🧬 Tertiary Structure: The 3D Shape of Proteins

The tertiary structure of proteins results in a compact, three-dimensional shape. Large proteins often consist of multiple protein domains that fold independently. The structure is influenced by the distribution of polar and nonpolar amino acids in the chain. Nonpolar side chains aggregate in the protein’s interior to avoid water, while polar side chains interact with the aqueous environment outside. Tertiary structures are critical for the protein's stability and function, as the hydrophobic core helps maintain its overall shape.

🔄 Protein Folding and Final Structure

Protein folding begins with the formation of secondary structures. Next, a hydrophobic collapse occurs, where nonpolar amino acids group together to avoid water. Long-range interactions between secondary structures lead to further folding, potentially passing through intermediate states like the molten globule state. This process is essential for reaching the final functional form of the protein.

🧩 Classes of Proteins: Globular, Fibrous, and Membrane

Proteins are categorized into three main classes based on their shape and solubility: globular, fibrous, and membrane proteins. Globular proteins are spherical, highly soluble in water, and structurally marginally stable, which allows for flexibility and function. Fibrous proteins, on the other hand, have linear, simple structures that provide support and are insoluble. Membrane proteins are associated with cell membranes, playing roles in various cellular functions.

Keywords

💡Polypeptide

A polypeptide is a chain of amino acids linked together by peptide bonds. In the video, polypeptides are described as the fundamental structures that fold to form proteins. The polypeptide backbone provides structural integrity, while side chains of amino acids determine the chemical properties and behavior of the protein.

💡Amino Acids

Amino acids are the building blocks of proteins, with 20 different types, each possessing unique chemical properties. They link together via covalent bonds to form polypeptide chains. The video emphasizes how the sequence of amino acids dictates the protein's final structure and function, with their side chains determining if they are polar or nonpolar.

💡Peptide Bonds

Peptide bonds are the covalent bonds that link amino acids together to form polypeptide chains. In the context of the video, these bonds create the polypeptide backbone of proteins, allowing the chain to fold into different structures while maintaining its integrity through these bonds.

💡Secondary Structure

Secondary structure refers to the localized folding patterns in a protein, including alpha helixes and beta sheets. These structures form due to hydrogen bonding between adjacent amino acids. The video explains how these are among the first folding patterns to emerge as proteins assemble.

💡Alpha Helix

An alpha helix is a type of secondary protein structure where the polypeptide chain coils into a spiral. It forms due to hydrogen bonding between NH groups and C=O groups of peptide bonds, creating a stable, spring-like structure. In the video, this is highlighted as a common folding pattern in proteins.

💡Beta Sheet

A beta sheet is a secondary protein structure that consists of polypeptide chains aligned side by side, forming parallel or antiparallel sheets. The video contrasts this with the alpha helix, explaining that hydrogen bonds stabilize beta sheets in a different manner by forming between strands rather than within a strand.

💡Tertiary Structure

The tertiary structure of a protein is its overall three-dimensional shape, formed after secondary structures have folded further. The video describes how tertiary structures result from interactions between amino acid side chains, including hydrophobic interactions that drive the folding process.

💡Hydrophobic Collapse

Hydrophobic collapse is a stage in protein folding where nonpolar (hydrophobic) amino acids aggregate to minimize their exposure to water. In the video, this phenomenon is explained as being central to determining the final folded shape of the protein, since nonpolar amino acids tend to be buried inside the protein.

💡Quaternary Structure

Quaternary structure refers to proteins that consist of more than one polypeptide chain, known as subunits. The video explains that quaternary structures form when multiple subunits interact, creating a functional protein complex.

💡Protein Folding

Protein folding is the process by which a polypeptide chain acquires its functional three-dimensional structure. The video details how folding involves multiple steps, starting with secondary structures and progressing through hydrophobic collapse and long-range interactions, sometimes passing through intermediate states like the molten globule.

Highlights

Proteins are made up of folded polypeptide chains composed of 20 different amino acids with varying chemical properties.

Amino acids are linked via covalent peptide bonds, forming the polypeptide backbone, with side chains giving unique chemical properties.

Protein structure is categorized into four levels: primary, secondary, tertiary, and quaternary.

The primary structure is the sequence of amino acids in the polypeptide chain and determines higher structural orders.

Secondary structure is formed through hydrogen bonds between adjacent amino acids, creating alpha helices and beta pleated sheets.

Tertiary structure results in a more compact, three-dimensional shape, often involving multiple protein domains.

Quaternary structure occurs when proteins consist of two or more interacting polypeptide chains (subunits).

Alpha helices form when the polypeptide chain coils like a spring, with specific hydrogen bonding patterns between peptide bonds.

Beta sheets can be parallel or anti-parallel, formed by neighboring chains running in the same or opposite directions.

Protein folding involves a hydrophobic collapse, where nonpolar amino acids aggregate, minimizing disruption to water molecules.

Polar amino acids tend to face the exterior of the protein, forming hydrogen bonds with surrounding water molecules.

Nonpolar amino acids are typically found in the interior of proteins, helping stabilize the folded structure.

The process of protein folding likely involves intermediate stages, such as a molten globule state.

Proteins are classified into three basic types based on shape and solubility: globular, fibrous, and membrane proteins.

Globular proteins are spherical, highly soluble in water, and marginally stable, facilitating motion and function.

Transcripts

proteins are made up of folded

polypeptide chains which are composed of

20 different amino acids each with

different chemical properties that are

linked to each other via covalent

peptide bonds the sequence of atoms

repeating to form the peptide bonds is

called the polypeptide backbone the

sidechain of each amino acid which is

the part that makes it different from

the other 19 amino acids can be either

polar or nonpolar

the polypeptide chain can fold in many

different ways called confirmations

confirmations are the spatial

arrangement of atoms that can result

from movement of atoms without breaking

of bonds protein structure can be

described in terms of four levels of

organization primary secondary tertiary

and quaternary structure the primary

structure is simply the amino acid

sequence of the polypeptide chain and it

is important to remember that this

sequence contains all the information

necessary for the higher orders of

structure the secondary structure is

formed by hydrogen bond interactions of

adjacent amino acids large numbers of

such local interactions form alpha

helixes and beta pleated sheets the

tertiary structure is a more compact

three-dimensional shape large proteins

often consists of several protein

domains which are distinct structural

units that fold somewhat independently

from one another

quaternary structure is found in those

proteins that have two or more

interacting polypeptide chains which are

then termed subunits

secondary structures include alpha

helixes and beta sheets an alpha helix

occurs where a polypeptide chain coils

like a spring with one turn every 3.6

amino acids in alpha helix ease the NH

of a peptide bond is hydrogen bonded to

the C double bond o of another peptide

bond which is one coil up in the helix

structure note also that all the NH

groups point in one direction towards

the end terminus and all the C double

bond o groups point in the opposite

direction towards the C terminus and

this is what gives the polypeptide chain

polarity the C terminus is partially

positively charged while the end

terminus is partially negatively charged

beta sheets conform parallel chains

which are made from neighboring chains

running in the same direction or anti

parallel chains which are made from a

polypeptide chain that folds back and

forth on itself so that nearby sections

run in opposite directions while

hydrogen bonds in an alpha helix our

interest Rand hydrogen bonds in beta

sheets are inter strand

tertiary structure formation can be

nucleated by the pattern of polar and

nonpolar amino acids in a polypeptide

chain which plays a central role in

determining the proteins final

confirmation this is because hydrophobic

molecules such as the nonpolar side

chains of certain amino acids are

entropically driven together in an

aqueous environment this limits their

disruption of the hydrogen bonding of

surrounding water molecules as a result

nonpolar amino acids tend to be found

predominantly in the interior of

proteins meanwhile polar amino acids

face the outside of the protein forming

hydrogen bonds with one another and with

the water molecules around the protein

those polar amino acids that are on the

inside of the protein bond with one

another or with the polypeptide backbone

it is thought that protein folding

happens roughly along the following

lines secondary structures form first

hydrophobic collapse during which

nonpolar amino acids aggregate happens

next

long-range interactions between

secondary structures cause further

folding to occur throughout this process

there may be one or more intermediate

states such as what has been termed a

molten globule

as a final note there are three basic

classes of proteins which are

distinguished based on shape and

solubility globular fibrous and membrane

proteins globular proteins are spherical

in shape with as little surface area per

volume as possible these proteins are

marginally stable and this marginal

stability facilitates motion which in

turn enables function hydrophilic amino

acids occupy this small surface area

making these proteins highly soluble in

water fibrous amino acids are simple

linear structures which have structural

roles and are insoluble lastly membrane

proteins are associated with cell

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