Proteins Simulation

Proteins Simulation Visually

Learn about proteins with interactive visualizations and simulations. Explore amino acids, protein structure (primary, secondary, tertiary, quaternary), folding mechanisms, and their diverse roles in biological systems.

Proteins Amino Acid Chains Protein Structure Folding & Function Enzymatic Activity Molecular Interactions Visual Simulation
Intro
Simulations
Calculators
Visualizations
Exercises
lJc

Introduction to Proteins

Proteins are large, complex biomolecules composed of amino acids linked by peptide bonds. They perform a vast array of functions within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another.

Key Concepts:

  • Amino Acids: Building blocks of proteins with central carbon, amino group, carboxyl group, and variable R group
  • Peptide Bond: Covalent bond formed between amino acids during protein synthesis
  • Protein Structure: Four levels of organization (primary, secondary, tertiary, quaternary)
  • Protein Folding: Process by which a protein assumes its functional shape

Biological Functions:

  • Enzymatic: Catalyze biochemical reactions
  • Structural: Provide support and shape to cells and tissues
  • Transport: Move molecules across membranes and in blood
  • Regulatory: Control gene expression and cellular processes

Interactive Protein Simulations

Amino Acid Structure Simulation

7.0

Protein Folding Simulation

37°C
0%

Secondary Structure Simulation

3

Enzyme Kinetics Simulation

50 mM
1 μM

Protein Calculators

Protein Molecular Weight Calculator

Results:

Total Residues: 100

Estimated MW: 11000 Da

Actual MW: 10890 Da

Isoelectric Point Calculator

Results:

pI: 6.8

Charge at pH 7: Negative

pKa Values: See details

Protein Concentration Calculator

Results:

Concentration: 50 μM

mg/mL: 6.6 mg/mL

Dilution Factor: 1

Protein Visualizations

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

Differences with Related Molecules

Proteins vs. Carbohydrates

Proteins: Nitrogen-containing polymers of amino acids, diverse functions, complex structures.

Carbohydrates: Carbon, hydrogen, oxygen polymers, primarily for energy and structure, simpler structures.

Proteins vs. Nucleic Acids

Proteins: Functional molecules built from amino acids, perform most cellular functions.

Nucleic Acids: Information storage and transfer molecules built from nucleotides.

Proteins vs. Lipids

Proteins: Hydrophilic/hydrophobic nature, structural and catalytic functions.

Lipids: Primarily hydrophobic, energy storage and membrane structure.

Example Exercises

Problem: Identify the properties of alanine and predict its behavior in different pH environments.

Scenario: Alanine has a simple methyl group as its R-group.

Task: Predict the charge state of alanine at pH 2, 7, and 11.

Solution:

At pH 2: Positively charged (+1) due to protonated amino group. At pH 7: Zwitterion (net charge 0) with protonated amino and deprotonated carboxyl. At pH 11: Negatively charged (-1) due to deprotonated carboxyl group.

Problem: Explain the factors that drive protein folding.

Scenario: A newly synthesized polypeptide chain must fold into its native conformation.

Task: Describe the forces involved in protein folding.

Solution:

Protein folding is driven by hydrophobic interactions (nonpolar residues cluster internally), hydrogen bonding, van der Waals forces, and disulfide bridges. The process is thermodynamically favorable as it minimizes free energy and maximizes stability.

Problem: Calculate the Vmax and Km values from enzyme kinetics data.

Scenario: An enzyme follows Michaelis-Menten kinetics.

Task: Interpret kinetic parameters and their significance.

Solution:

Vmax represents the maximum reaction rate when enzyme is saturated with substrate. Km is the substrate concentration at which reaction rate is half of Vmax. loW Km indicates high affinity for substrate.

Multiple Choice Questions

1. How many different amino acids are commonly found in proteins?
2. The α-helix structure is stabilized by:
3. The primary structure of a protein refers to:
4. Which level of protein structure involves interactions between multiple polypeptide chains?
5. The isoelectric point (pI) of a protein is:
6. Which amino acid contains a sulfur atom?

Export/Import Data

Hover Effect Visualizations

Amino Acids

Hover to see structure

Structure

Hover to see folding

Enzymes

Hover to see activity

Complexes

Hover to see interactions