How Enzymes/Proteins Work at Atomic/Molecular Level

In summary, the conversation discusses the concept of enzymes and proteins on a molecular level and the role they play in cellular processes. Specifically, the conversation focuses on ATP synthase and how it works as a "waterwheel" to produce ATP. The conversation also mentions other types of enzymes, such as kinases, and their role in cellular control and regulation.
  • #1
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So I've learned in biology about the amino acids forming chains/trees, and having different interacting "R groups"
Can somebody link to me an animation or careful description of how a specific enzyme/protein moves its parts step by step on an atomic/molecular level? I cannot find one.
I want to have an idea about how such tiny "machines" can work with only a few thousand atoms, and if I see one specific example I think I will understand how this works better.
Thank you
 
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  • #2


This is ATP synthase. The top portion acts like a waterwheel of sorts that sits in the inner mitochondrial membrane. Via the electron transport chain, protons are built up on the outside and the only way to get to the inside is through the "waterwheel". That force (because they're trying to reach equilibrium) spins the top part around and the shaft that it's connected to. The rotation of the shaft shifts the bottom domains back and forth so when ADP and a phosphate ion bind when the active site is open, it pinches them together when it closes, binding them and making ATP.

I hope that helped.
 
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  • #3
aroc91 said:


This is ATP synthase. The top portion acts like a waterwheel of sorts that sits in the inner mitochondrial membrane. Via the electron transport chain, protons are built up on the outside and the only way to get to the inside is through the "waterwheel". That force (because they're trying to reach equilibrium) spins the top part around and the shaft that it's connected to. The rotation of the shaft shifts the bottom domains back and forth so when ADP and a phosphate ion bind when the active site is open, it pinches them together when it closes, binding them and making ATP.

I hope that helped.


Yes, this is the sort of thing I was talking about!
Very interesting video... I didn't understand how mechanical enzymes could be
 
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  • #4
Not all enzymes have such dramatic mechanical motions. Kinases are good examples. They takes a phosphate group from ATP and attaches it to one of the side chains (aka 'R groups') on another protein, the substrate:


Here, the enzyme activity isn't as mechanical, its chemical. The substrate and the enzyme have complimentary charges and geometry, so that only specific substrates can get close enough, and hang around long enough, for the phophate to be transferred.

This is also a great example of cellular control. It effectively allows computations to be done by taking in inputs (the regulatory proteins, such as cyclin or inhibitors) and gives an output (either the substrate is phosphorylated or it isn't).
 
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  • #5
for your question. Enzymes and proteins are essential components of all living organisms and play crucial roles in various biological processes. These molecules are made up of long chains of amino acids, which are linked together by peptide bonds. The sequence and arrangement of these amino acids determine the shape and function of the enzyme/protein.

At the atomic/molecular level, enzymes and proteins work by binding to specific molecules, called substrates, and facilitating chemical reactions. This binding occurs at the active site of the enzyme, which is a specific region that is complementary in shape and chemical properties to the substrate. This specific binding is made possible by the unique arrangement of amino acids in the active site.

Once the substrate binds to the active site, the enzyme undergoes a conformational change. This means that the shape of the enzyme is altered in a way that brings the substrate closer to each other, facilitating the chemical reaction. This conformational change is often referred to as induced fit.

The enzyme then catalyzes the chemical reaction by lowering the activation energy required for the reaction to occur. This is achieved through the precise positioning of the substrate and the involvement of specific amino acids in the active site that act as catalysts.

After the reaction is complete, the products are released from the enzyme and it returns to its original shape. The enzyme can then bind to another substrate and repeat the process.

To understand this process better, I recommend watching this animation by the Howard Hughes Medical Institute: . It demonstrates the step-by-step process of enzyme action at the atomic/molecular level using the example of an enzyme called lysozyme.

In summary, enzymes and proteins are able to work at the atomic/molecular level due to their precise structure and the specific interactions between their amino acids and the substrate. This allows them to act as efficient and specific catalysts in biological reactions, despite being made up of only a few thousand atoms. I hope this helps to clarify how these tiny "machines" work in living organisms.
 

1. How do enzymes/proteins function at the atomic/molecular level?

Enzymes and proteins function at the atomic/molecular level by utilizing their specific three-dimensional structures to bind with specific substrates. This binding allows for chemical reactions to occur, either by breaking down larger molecules or creating new ones. Enzymes and proteins also have specific active sites where the substrate can bind, allowing for precise and efficient reactions to take place.

2. What role do amino acids play in enzyme/protein function?

Amino acids are the building blocks of enzymes and proteins. The sequence of amino acids determines the three-dimensional structure of the enzyme/protein, which in turn determines its function. Different amino acid sequences result in different structures and functions, allowing for a wide range of enzymes/proteins to exist and carry out specific tasks in the body.

3. How do enzymes/proteins lower the activation energy of a reaction?

Enzymes and proteins lower the activation energy of a reaction by stabilizing the transition state of the reaction. The active site of the enzyme/protein binds with the substrate, creating an enzyme-substrate complex. This alters the chemical bonds within the substrate, making it easier to reach the transition state and undergo the desired reaction. This ultimately lowers the activation energy and allows the reaction to occur more quickly.

4. What factors can affect enzyme/protein function at the atomic/molecular level?

Several factors can affect enzyme/protein function at the atomic/molecular level. These include temperature, pH, and the presence of inhibitors or activators. Enzymes and proteins have specific optimal conditions under which they can function efficiently. Deviations from these conditions can alter the enzyme/protein's structure and affect its ability to bind with substrates and carry out reactions.

5. How are enzymes/proteins able to carry out specific reactions?

Enzymes and proteins are able to carry out specific reactions due to their unique structures and specific active sites. The shape of the active site is complementary to the shape of the substrate, allowing for precise binding and reaction to occur. Additionally, the amino acid sequence and chemical properties of the active site contribute to the enzyme/protein's specificity for certain substrates and reactions.

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