Name: how protein shape determines function
Uploaded: 2023-04-30T18:28:47.000Z
Duration: 2 min 15 s
Channel: JoVE

K12 Standards

Next Generation Science Standards

High School

Life Science

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

HS-LS1-1

Protein and Protein Structures

Proteins are polymers of amino acids linked together through peptide bonds. Most proteins fold into specific three-dimensional structures to perform their function.
Protein structure is classified into four categories: primary, secondary, tertiary, and quaternary.
The linear sequence of amino acids in the protein is its primary structure. These sequences are read in the polymer synthesis order, from the N-terminal, the free amino end, to the C-terminal, the free carboxyl end.
Secondary structures form through hydrogen bonding between the oxygen from the carbonyl group of one amino acid and the hydrogen from the amino group of another. Common secondary structures include &#945;-helices and &#946;-pleated sheets.&#160;
These and other connecting structures, such as &#946;-turns, further interact to form the protein&#8217;s three-dimensional structure, known as the tertiary structure.
The formation of the tertiary structure occurs due to interactions between the R-groups of the amino acids.
R-groups with opposite charges can form ionic bonds, and sulfur in two cysteines can form a covalent disulfide bridge. Other contributors include hydrophobic interactions between hydrophobic side chains and hydrogen bonds between polar side chains.
Additionally, some proteins form quaternary structures, assemblies of two or more polypeptide chains. For example, hemoglobin is a protein made up of four subunits, two &#945; and two &#946;.
Scientists can use the structure of a protein to predict its function and location in a cell. Proteins in the cell cytoplasm have hydrophilic amino acids on their surfaces that interact with the water in the cytoplasm and have hydrophobic cores.
In contrast, proteins present in cell membranes often have hydrophobic amino acids on the surface that interact with glycerophospholipids in the membrane and have hydrophilic cores.&#160;

protein and protein structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein&#39;s shape is critical to its function. For example, an enzyme can bind a specific substrate at its active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.
Primary Structure
Amino acids&#39; unique sequence in a polypeptide chain is its primary structure. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine; whereas, the C terminal amino acid is asparagine.&#160; The amino acid sequences in the A and B chains are unique to insulin.
The gene encoding the protein ultimately determines the unique sequence for every protein. A change in the nucleotide sequence of the gene&#8217;s coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin &#946; chain has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the &#946; chain substitutes the amino acid glutamic acid. Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or &#8220;sickle&#8221; shape, which clogs blood vessels. This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.
Secondary Structure
The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common are the &#945;-helix and &#946;-pleated sheet structures. Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.
Every helical turn in an alpha helix has 3.6 amino acid residues. The polypeptide&#39;s R groups (the variant groups) protrude out from the &#945;-helix chain. In the &#946;-pleated sheet, hydrogen bonding between atoms on the polypeptide chain&#39;s backbone forms the &#34;pleats&#34;. The R groups are attached to the carbons and extend above and below the pleat&#39;s folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone&#39;s carbonyl group. The &#945;-helix and &#946;-pleated sheet structures are in most globular and fibrous proteins, and they play an important structural role.
Tertiary Structure
The polypeptide&#39;s unique three-dimensional structure is its tertiary structure. This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein&#39;s complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other, and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids&#39; hydrophobic R groups lie in the protein&#39;s interior; whereas, the hydrophilic R groups lie on the outside. Interactions between cysteine side chains form disulfide linkages in the presence of oxygen, the only covalent bond that forms during protein folding.
All of these interactions, weak and strong, determine the protein&#39;s final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional.
Quaternary Structure
In nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulfide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulfide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a &#946;-pleated sheet structure that is the result of hydrogen bonding between different chains.
This text has been adapted from <a href="https://openstax.org/books/biology-2e/pages/3-4-proteins">Openstax, Biology 2e, Chapter 3.4: Proteins</a>.

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may ...

Education

JoVE Core

Cell Biology

Unit 1

Biochemistry of the Cell

KEY TERMS AND CONCEPTS

how protein shape determines function

Proteins are essential molecules in living things, and their shape affects how they work. Protein structure is described at several levels, including primary, secondary, tertiary, and quaternary structure. These levels help explain how a protein is built and how its final form supports its job.

Primary structure is the sequence of amino acids in a protein. Secondary structure forms when parts of the chain fold into regular patterns. Tertiary structure is the overall three-dimensional shape of one protein chain. Quaternary structure appears when more than one protein chain joins together to make a working protein.

The video also shows how protein structure can be represented in different ways. A simple line drawing can show the amino acid sequence. Other models can show folding and the full 3D shape. These visual forms help students compare levels of structure and see why protein shape matters.

How Protein Shape Determines Function

the periodic table and organismal elements

the-periodic-table-and-organismal-elements

Elements in the Human Body and Periodic Table

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functional groups

Functional Groups in Organic Molecules

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noncovalent attractions in biomolecules

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Proteins are essential molecules in living things, and their shape affects how they work. Protein structure is described at several levels, including primary, secondary, tertiary, and quaternary structure. These levels help explain how a protein is built and how its final form supports its job. Primary structure is the sequence of amino acids in a protein. Secondary structure forms when parts of the chain fold into regular patterns. Tertiary structure is the overall three-dimensional shape of...

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key terms and concepts

Learn how proteins are built and folded through primary, secondary, tertiary, and quaternary structure, and how protein shape affects function.

How Protein Shape Determines Function | JoVE K12

cell biology

JoVE Core Cell Biology illustrates complex cellular processes in easy-to-understand yet comprehensive animated video lessons. This collection focuses on the essential components and functions of cells, including organelles and membranes, cellular transport, and cell energetics. It is complemented by scientist-in-action videos that demonstrate the application of cell biology in real-world research experiments.

Florida Department of Education

SC.912.L.18

SC.912.L.18.1

SC.912.L.18.4

new-york-state-science-learning-standards

New York State Science Learning Standards

Structure and Function

HS-LS1-1.

Georgia Standards of Excellence

9-12

Biology

SB6.c

Characteristics of Life

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protein-complexes-with-interchangeable-parts

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Mechanical Protein Function

Structural Protein Function

Protein Networks

Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins, which carry out the essential functions of life through systems of specialized cells. [Assessment Boundary: Assessment does not include identification of specific cell or tissue types, whole body systems, specific protein structures and functions, or the biochemistry of protein synthesis.]

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Develop and use a model to illustrate the hierarchical organization of interacting systems that provide specific functions within multicellular organisms. [Clarification Statement: Emphasis is on functions at the organism system level such as nutrient uptake, water delivery, and organism movement in response to neural stimuli. An example of an interacting system could be an artery depending on the proper function of elastic tissue and smooth muscle to regulate and deliver the proper amount of blood within the circulatory system.] [Assessment Boundary: Assessment does not include interactions and functions at the molecular or chemical reaction level.]

HS-LS1-2

How Protein Shape Determines Function

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