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Protein Structure

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Protein Structure and Folding

After a polypeptide is produced in protein synthesis, it's not necessarily a functional protein yet! Explore protein folding that occurs within levels of protein structure with the Amoeba Sisters! Primary, secondary, tertiary, and quaternary protein structure levels are briefly discussed. Video also mentions chaperonins (chaperone proteins) and how proteins can be denatured.

Table of Contents:
00:00 Intro
0:41 Reminder of Protein Roles
1:06 Modifications of Proteins
1:25 Importance of Shape for Proteins
1:56 Levels of Protein Structure
2:06 Primary Structure
3:10 Secondary Structure
3:45 Tertiary Structure
4:58 Quaternary Structure [not in all proteins]
6:01 Proteins often have help in folding [introduces chaperonins]
6:40 Denaturing Proteins

*Further Reading Suggestions*

Related to Protein Misfoldings:




Learn About The Protein Folding Problem:



Factual References:

OpenStax, Biology. OpenStax CNX. Jun 1, 2018

Reece, J. B., & Campbell, N. A. (2011). Campbell biology. Boston: Benjamin Cummings / Pearson.


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Protein Structure

Everyone has heard of proteins. What are they on the molecular level? They're polymers of amino acids, of course. They make up most of your body, so we have to understand their structure very well! Check this out to learn the hierarchy of protein structure so that we can later learn all about what different types of proteins can do.

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Protein Structure - Primary, Secondary, Tertiary, & Quarternary - Biology

This biology video tutorial provides a basic introduction into the four levels of protein structure - primary, secondary, tertiary and quarternary structure. The primary structure of a protein is based on the sequence of amino acids. The secondary structure is based on localized shapes such as the alpha helix or the beta pleated sheet. The tertiary structure of a protein describes its three-dimensional folding pattern. A tertiary structure contains one individual subunit where as a quarternary structure has multiple subunits.

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Four levels of protein structure | Chemical processes | MCAT | Khan Academy

The four levels of protein structure are primary, secondary, tertiary, and quaternary. It is helpful to understand the nature and function of each level of protein structure in order to fully understand how a protein works. By Tracy Kovach. Created by Tracy Kim Kovach.

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Protein structure | Primary | Secondary | Tertiary | Quaternary

Primary structure is the linear sequence of amino acids written from the N termial of first to the C terminal of the last amino acid. The information of the primary structure is obtained by sequencing the gene or the protein. The primary structure further folds to form secondary structure. The most common secondary structure is the alpha helix and the beta sheet. secondary structure further forms tertiary structure. Interaction between tertiary structure forms quaternary structure.

Protein structure | primary secondary tertiary and quaternary structure of protein

Protein structure - This lecture explains about the protein structure hierarchy including primary, secondary, tertiary structures of protein. All the types of protein structures are explained in this video with example. So watch this video to understand alpha helix and beta sheet structure and the role of primary structure of the protein to make 3d protein which dictates the function of the protein.
So keep watching this video for knowing the following details
1. Primary structure of protein
2. Secondary structure of protein
3. Tertiary structure of the protein
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Thank you for watching the video lecture on protein structure.

Protein - Structure Of Protein - What Is Protein Made Of - Structure Of Amino Acids Building Blocks

In this video we discuss the structure of protein and the structure of amino acids. We cover how amino acids link together to form proteins.



Transcript/notes

Protein structure

All Proteins contain 4 elements, carbon, hydrogen, oxygen and nitrogen, however, some proteins contain phosphorus, sulfur, iron, zinc, magnesium and other trace metals. Proteins are giant macro molecules that are made up of amino acid building blocks. Amino acids can link together to form long chains, typically a protein consists of 100 or more amino acids linked together.

There are 20 different standard amino acids that your body requires for healthy function. These amino acids are often classified as essential and non-essential amino acids.

Nonessential amino acids are amino acids that our bodies can produce even if we don’t get them from the food we eat. There are 11 non-essential amino acids (list). Essential amino acids cannot be made by the body, so, they must come from foods we eat. There are 9 essential amino acids.

The basic structure of amino acids is that they consist of a alpha carbon, a carboxyl group, which is a carbon, oxygen, hydrogen, hydrogen group, a lone hydrogen atom, an amino group, which is a nitrogen, hydrogen, hydrogen group, and a side chain or functional group, which is often referred to as an R-group. The formation of the side chain is what makes amino acids different from one another.

On the screen is the structural formulas for all 20 of the standard amino acids along with the amino acid selenocysteine, as some sources list it as a 21st standard amino acid. As you can see, they all have the same chemical backbone, and the only difference is their unique functional R group.

These functional R groups of have chemical characteristics that allow amino acids to be organized into groups.
Here we have the non polar amino acids, non polar meaning the electrons are shared equally in the molecule, these are hydrophobic, so they tend to be repelled from water.

Here are the polar amino acids; these molecules can have interactions with other polar amino acids and with water molecules.

Here are the charged amino acids, since they are charged, an ionic bond can form between an R group with a negative charge and an R group with a positive charge.

And here are some amino acids that are considered to have unique structures.

As was stated earlier, amino acids can link together to form long chains, there is an almost infinite number of different variations of chains that can be formed from amino acids. Each chain can have different characteristics with different chemical properties.

When 2 amino acids join together they form what is called a peptide bond. A peptide bond is when the carboxyl or carbon, oxygen, hydrogen, hydrogen group of one amino acid bonds with the amino nitrogen, hydrogen, hydrogen group of another amino acid, as you can see here (on screen).

This is done through a dehydration synthesis reaction, as the amino group involved in the bond loses a hydrogen atom, and the carboxyl group involved in the bond loses an oxygen and hydrogen. So, the peptide bonding results in the release of a water h2o molecule. More amino acids can link in, again releasing water molecules, and form what is called a polypeptide chain.

As you can see in this polypeptide chain, at one end, an amino group remains, called the N terminal, and at the other end a carboxyl group remains, the C terminal. Typically a protein consists of 100 or more amino acids linked together. Some proteins are single polypeptide chains, and other proteins have polypeptide chains linked together.

Individual amino acids can also be released from a peptide chain, by the decomposition reaction hydrolysis. In hydrolysis, a water molecule is added, breaking the peptide bond and freeing up amino acids.

So, amino acids link together in a variety of sequences to form different types of proteins. Some of these proteins serve as enzymes, which help speed up metabolic reactions in the body, some serve as hormones and help regulate certain functions in the body, some proteins help form the structure of various tissues in the body, these are just a few of the many, many functions that proteins have in the body.

Proteins

Paul Andersen explains the structure and importance of proteins. He describes how proteins are created from amino acids connected by dehydration synthesis. He shows the importance of chemical properties in the R-groups of individual amino acids in the polypeptide. He explains the four levels of protein folding and gives you an opportunity to fold proteins of your own using the game Foldit:

Download the video game foldit here:



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Overview of protein structure | Macromolecules | Biology | Khan Academy

Primary, secondary, tertiary and quaternary protein structure. Thinking about how the different factors impacting a protein's structure. Beta pleated sheets. Alpha helices.

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Proteins and their Structure

MBD Alchemie presents a video that talks about the structure of proteins, classification of the proteins on the basis of their structure and molecular shape.

Learn about proteins and their structure through this video.

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Proteins and their Structure

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12. Introduction to Protein Structure; Structure Comparison and Classification

MIT 7.91J Foundations of Computational and Systems Biology, Spring 2014
View the complete course:
Instructor: Ernest Fraenkel

Professor Ernest Fraenkel begins his unit of the course, which moves across scales, from atoms to proteins to networks. This lecture is about the structure of proteins, and how biological phenomena make sense in light of protein structure.

License: Creative Commons BY-NC-SA
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Protein Shape - Levels Of Protein Structure - Shape Of Proteins - What Is Protein Denaturation

In this video we discuss the 4 different levels of protein shape, as we cover primary, secondary, tertiary or the third level, and quaternary or the fourth level. We also discuss the denaturation of protein and some things that cause it.



Protein shape

There are 4 different levels of protein structure, or protein shape. Primary, secondary, tertiary or the third level, and quaternary or the fourth level.

The primary or 1st level of protein structure is a chain like or linear sequence of amino acids joined by peptide bonds as you see here.
The secondary or 2nd level has 2 shapes, an alpha helix or coil like formation, or folded pattern called a beta sheet. In both of these structures hydrogen bonds between the amino acids stabilize the shape of the protein.

The tertiary or 3rd level of protein structure involves more folding and bonding of the secondary structure. The coils may even touch each other as some covalent bonds form from the sharing of electrons between different amino acids, but most of these twists and folds occur from the result of ionic bonds between positively and negatively charged r groups of amino acids.

The quaternary or 4th level is where clusters of more than one polypeptide chain link together to form a giant molecule. Many different types of bonds may be formed within this structure.
The shape of a protein is important, for instance, fibrous proteins are extended linear proteins that are part of ligaments, tendons and muscles, and globular proteins fold into almost spherical shapes and have their hydrophobic or water fearing r groups buried deep within the core, and their hydrophilic or water loving r groups extended out into the water when in an aqueous environment.

Proteins take their shape based on the job they are required to perform and some have moving parts that are important to their functions.

Proteins can have their structure or shaped by denaturation. When this happens, the protein is no longer able to carry out its job. Denaturation can take place because of change of temperature, change in pH, or in the presence of certain hazardous chemicals.

What is a Protein? Learn about the 3D shape and function of macromolecules

A new version of this video is available at

Proteins play countless roles throughout the biological world, from catalyzing chemical reactions to building the structures of all living things.

Despite this wide range of functions all proteins are made out of the same twenty amino acids, but combined in different ways. The way these twenty amino acids are arranged dictates the folding of the protein into its unique final shape. Since protein function is based on the ability to recognize and bind to specific molecules, having the correct shape is critical for proteins to do their jobs correctly.

A PDF flyer accompanies this video at PDB-101 at

Animation by Maria Voigt, narration by Monica Sekharan

Protein Structure and Function - Part 1

This lesson provides an overview of the structure of proteins and their amino acid building blocks.

Proteins: Amino Acids, Polypeptides, and the Four Levels of Protein Structure

In this video, Mr. W explains the key aspects of protein structure and function. The video covers
1. The general structure of amino acids.
2. How amino acids can differ based on their side chains.
3. How amino acids link by peptide bonds to form polypeptides
4. The four levels of protein structure.
Throughout, the focus is on how protein structure can be both specific and dynamic.

The video links to an interactive tutorial at


The quizzes discussed in the video are:
Proteins quiz 1: tinyurl.com/yypqzc3g
Proteins quiz 2: tinyurl.com/y47zhh5y

Other tutorials discussed in this video:
Carbon and Functional Groups:


The material in this video covers AP Biology Topics 1.3 and 1.4.
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Proteins: Primary and Secondary Structure | A-level Biology | OCR, AQA, Edexcel

Proteins: Primary and Secondary Structure in a Snap! Unlock the full A-level Biology course at created by Adam Tildesley, Biology expert at SnapRevise and graduate of Cambridge University.

SnapRevise is the UK’s leading A-level and GCSE revision & exam preparation resource offering comprehensive video courses created by A* Oxbridge tutors. Our courses are designed around the OCR, AQA, SNAB, Edexcel B, WJEC, CIE and IAL exam boards, concisely covering all the important concepts required by each specification. In addition to all the content videos, our courses include hundreds of exam question videos, where we show you how to tackle questions and walk you through step by step how to score full marks.

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The key points covered in this video include:

1. Primary Structure
2. Secondary Structure

Primary Structure of Proteins

Every protein has a unique shape, allowing them all to carry out different functions in organisms. When a polypeptide is made, the order of the amino acids determines the primary structure of the protein. The primary structure of a protein is the sequence of amino acids. Most polypeptide chains are made up of many hundreds of amino acids. There are 20 different naturally occurring amino acids, resulting in trillions of potential combinations. The almost limitless number of combinations allows every protein to have a completely unique primary structure.

Secondary Structure of Proteins

The polypeptide chains formed from joining amino acids together are not always straight. Instead sections of the chain can curl and fold into two main shapes: α- helixes, β-pleated sheets. These shapes arise as due to the structure of amino acids - they all contain a -C=O group and a -NH group when bonded in a chain. The hydrogen in -NH is slightly positive and the oxygen in -C=O is slightly negative - this results in a hydrogen bond between amino acids. In an α- helix, the polypeptide chain coils with hydrogen bonds keeping the coil stable. In β-pleated sheets, the chains form a zig-zag and fold over themselves. Although hydrogen bonds are weak, the many hundreds of them keep the secondary structure stable. The secondary structure of a protein is the curling or folding of the polypeptide chain into α- helices and β-pleated sheets due to the formation of hydrogen bonds.

Protein Structure | Four levels of protein Organization | shape of protein (Biochemistry lecture)

Four Levels of Protein Structure
With the goal of understanding the function of a protein,
learning about its structure is often productive. In spite of
their great diversity, all proteins share three superimposed
levels of structure, known as primary, secondary, and tertiary
structure. A fourth level, quaternary structure, arises when a protein consists of two or more polypeptide chains.
The primary structure of a protein is its sequence of amino
acids.
Most proteins have segments of their polypeptide chains repeatedly
coiled or folded in patterns that contribute to the protein’s overall
shape. These coils and folds, collectively referred to as secondary
structure, are the result of hydrogen bonds between the repeating
constituents of the polypeptide backbone (not the amino acid
side chains). One such secondary structure is the ???????? helix, The other main type of secondary structure is the ???? pleated
sheet.
tertiary structure is the overall shape of a
polypeptide resulting from interactions between the side chains
(R groups) of the various amino acids.
Quaternary structure is the
overall protein structure that results from the aggregation of these
polypeptide subunits.
Many proteins are roughly spherical (globular proteins), while others are shaped like long fibers (fibrous proteins).

Structure of Proteins

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Primary Structure of Proteins

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Protein Structure - Primary - Secondary - Tertiary - Quaternary - Structure of Protein

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