Use standard one-letter codes (e.g., A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V). Case-insensitive.
Calculation Results
Sequence Length:— residues
Total Residue Mass:— Da
Water Molecules (n-1):—
Mass of Water (n-1):— Da
Molecular Weight: — Da
Formula Used: The molecular weight of a peptide sequence is calculated by summing the average molecular weights of each amino acid residue in the sequence and then subtracting the mass of water molecules lost during peptide bond formation. For a sequence of 'n' amino acids, (n-1) water molecules are removed. The formula is: MW = Σ(Residue MW) – (n-1) * MW(H₂O).
Mass Contribution by Residue Type
Amino Acid Residue MassWater Mass Removed
Amino Acid Residue Molecular Weights (Average)
One-Letter Code
Full Name
Average Molecular Weight (Da)
Understanding the Amino Acid Sequence Molecular Weight Calculator
What is Amino Acid Sequence Molecular Weight?
The molecular weight of an amino acid sequence, often referred to as peptide or protein molecular weight, is a fundamental property in biochemistry and molecular biology. It represents the total mass of a chain of amino acids linked together by peptide bonds. Each amino acid has a unique chemical structure and thus a specific molecular weight. When amino acids join to form a peptide or protein, they do so through a dehydration (condensation) reaction, where a molecule of water is released for each peptide bond formed. Therefore, the final molecular weight of the sequence is the sum of the individual amino acid residue weights minus the mass contributed by the released water molecules.
Who should use it: Researchers, students, biochemists, molecular biologists, pharmacologists, and anyone working with peptides and proteins will find this calculator invaluable. It's crucial for experimental design, data analysis, and understanding the physical properties of biomolecules.
Common misconceptions: A common misconception is that the molecular weight is simply the sum of the atomic weights of all atoms in the sequence. However, this ignores the mass lost during peptide bond formation. Another is confusing the "residue weight" (the weight of an amino acid *after* losing water) with the weight of a free amino acid. This calculator uses the standard average residue weights.
Amino Acid Sequence Molecular Weight Formula and Mathematical Explanation
The calculation of the molecular weight for an amino acid sequence is based on the principle of summing individual components and accounting for the mass changes during polymerization.
Step-by-step derivation:
Identify Amino Acids: The input is a sequence of amino acids represented by their one-letter codes (e.g., 'AGV').
Determine Residue Weights: For each amino acid in the sequence, find its corresponding average molecular weight as a residue (i.e., after losing a water molecule).
Sum Residue Weights: Add up the average molecular weights of all the amino acid residues in the sequence. Let this sum be Σ(Residue MW).
Count Peptide Bonds: A peptide sequence of 'n' amino acids contains (n-1) peptide bonds.
Calculate Total Water Mass Removed: Multiply the number of peptide bonds by the average molecular weight of a water molecule (approximately 18.015 Da). This gives (n-1) * MW(H₂O).
Calculate Final Molecular Weight: Subtract the total mass of water removed from the sum of the residue weights.
Formula:Molecular Weight (Da) = Σ(Average Residue Molecular Weight) - (Number of Amino Acids - 1) * Average Molecular Weight of Water (H₂O)
Variable Explanations:
Variable
Meaning
Unit
Typical Range / Value
Sequence
The string of one-letter amino acid codes.
N/A
e.g., 'GAV', 'PEPTIDE'
n
Number of amino acid residues in the sequence.
Residues
≥ 1
Σ(Average Residue MW)
Sum of the average molecular weights of each amino acid residue in the sequence.
Daltons (Da)
Varies based on sequence composition.
MW(H₂O)
Average molecular weight of a water molecule.
Daltons (Da)
~18.015 Da
(n-1)
Number of peptide bonds formed, equal to the number of water molecules removed.
Molecules
≥ 0
Molecular Weight (Da)
The final calculated average molecular weight of the peptide sequence.
Daltons (Da)
Varies widely.
Practical Examples (Real-World Use Cases)
Understanding the molecular weight is crucial for various applications, from mass spectrometry to protein purification.
Example 1: A Simple Tripeptide – Gly-Ala-Val
Inputs:
Sequence: GAV
Calculation Steps:
Sequence Length (n) = 3
Number of water molecules removed (n-1) = 2
Average MW of Glycine residue = 75.067 Da
Average MW of Alanine residue = 89.094 Da
Average MW of Valine residue = 117.147 Da
Sum of Residue MW = 75.067 + 89.094 + 117.147 = 281.308 Da
Mass of Water Removed = 2 * 18.015 = 36.030 Da
Molecular Weight = 281.308 – 36.030 = 245.278 Da
Interpretation: A short peptide composed of Glycine, Alanine, and Valine has a molecular weight of approximately 245.28 Daltons. This value is essential for identifying the peptide using mass spectrometry.
Example 2: A Short Peptide – Ala-Pro-Ser-Gly
Inputs:
Sequence: APSG
Calculation Steps:
Sequence Length (n) = 4
Number of water molecules removed (n-1) = 3
Average MW of Alanine residue = 89.094 Da
Average MW of Proline residue = 115.131 Da
Average MW of Serine residue = 105.093 Da
Average MW of Glycine residue = 75.067 Da
Sum of Residue MW = 89.094 + 115.131 + 105.093 + 75.067 = 384.385 Da
Mass of Water Removed = 3 * 18.015 = 54.045 Da
Molecular Weight = 384.385 – 54.045 = 330.340 Da
Interpretation: The peptide Ala-Pro-Ser-Gly has a molecular weight of approximately 330.34 Daltons. This precise mass is critical for confirming the peptide's identity and purity in experimental settings.
How to Use This Amino Acid Sequence Molecular Weight Calculator
Using this calculator is straightforward and designed for efficiency.
Enter the Sequence: In the "Amino Acid Sequence" input field, type the sequence using the standard one-letter codes for each amino acid. The input is case-insensitive (e.g., 'gav' is the same as 'GAV'). Ensure you use valid codes (A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V).
Calculate: Click the "Calculate" button. The calculator will process the sequence.
View Results: The results section will update in real-time to show:
Sequence Length: The total number of amino acids.
Total Residue Mass: The sum of the average molecular weights of all residues.
Water Molecules (n-1): The number of water molecules removed during peptide bond formation.
Mass of Water (n-1): The total mass contributed by the removed water molecules.
Molecular Weight: The final calculated average molecular weight of the peptide sequence in Daltons (Da).
Interpret the Data: The primary result, "Molecular Weight," is your key value. The intermediate values provide insight into the calculation process. The table shows the specific weights used for each amino acid. The chart visually represents the mass contribution of residues versus water.
Reset: If you need to start over or clear the fields, click the "Reset" button.
Copy Results: Use the "Copy Results" button to easily transfer the main result, intermediate values, and key assumptions to your notes or reports.
Decision-making guidance: The calculated molecular weight is vital for experimental planning. For instance, when setting up mass spectrometry experiments, knowing the expected mass helps identify the correct peaks. For protein purification, it can inform buffer conditions or column choices based on expected size.
Key Factors That Affect Amino Acid Sequence Molecular Weight Results
While the calculation itself is precise, several factors influence the interpretation and accuracy of the molecular weight:
Amino Acid Composition: The most significant factor. Sequences rich in heavier amino acids (like Tryptophan, Tyrosine, Phenylalanine) will have higher molecular weights than those rich in lighter ones (like Glycine, Alanine).
Sequence Length: Longer sequences naturally have higher molecular weights due to the cumulative addition of residue masses.
Isotopes: The calculator uses average molecular weights, which are based on the natural isotopic abundance of elements. Actual molecules will have specific isotopic masses, leading to slight variations, especially noticeable in high-resolution mass spectrometry.
Post-Translational Modifications (PTMs): Many proteins undergo modifications after synthesis (e.g., phosphorylation, glycosylation, acetylation). These add chemical groups, significantly increasing the molecular weight beyond the basic sequence calculation. This calculator does not account for PTMs.
N- and C-terminal Modifications: The N-terminus typically has an amino group (-NH2) and the C-terminus a carboxyl group (-COOH). The standard residue weights implicitly account for the loss of H from the N-terminus and OH from the C-terminus during peptide bond formation. However, if these termini are chemically modified (e.g., cyclization, capping), the mass will differ.
Proline's Unique Structure: Proline is an imino acid. Its side chain forms a ring with its own amino group. This affects peptide bond geometry and slightly alters its residue weight calculation compared to standard amino acids.
Accuracy of Residue Weights: The calculator uses standard average residue weights. Different sources might provide slightly different values based on the isotopic composition or specific chemical forms considered.
Frequently Asked Questions (FAQ)
What is the difference between molecular weight and mass?
In biochemistry, the terms "molecular weight" and "mass" are often used interchangeably, especially when expressed in Daltons (Da). Technically, mass is the amount of matter in a substance, while weight is the force of gravity on that mass. Molecular weight is a relative term, often referring to the sum of atomic weights. However, for practical purposes in this context, the calculated value in Daltons represents the mass of the molecule.
Why use average molecular weights?
Natural elements exist as isotopes with different masses. Average molecular weights are calculated based on the natural abundance of these isotopes. This provides a representative value for a typical molecule. High-resolution mass spectrometry can measure the exact mass of specific isotopic forms.
Does the calculator handle non-standard amino acids?
No, this calculator is designed for the 20 standard proteinogenic amino acids represented by the one-letter codes A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V. For non-standard amino acids or modified residues, you would need to manually find their specific residue weights and adjust the calculation.
What does 'Da' stand for?
'Da' stands for Dalton, the unit of molecular mass commonly used in biochemistry and molecular biology. One Dalton is approximately the mass of one hydrogen atom. It is numerically equivalent to the atomic mass unit (amu).
How does this relate to protein mass spectrometry?
The calculated molecular weight serves as a theoretical prediction. In mass spectrometry (like MALDI-TOF or ESI-MS), you measure the actual mass-to-charge ratio (m/z) of ionized peptides or proteins. Comparing the measured mass to the calculated theoretical mass is a primary method for identifying and verifying peptide sequences.
Can this calculator determine the mass of a whole protein?
Yes, if you input the complete amino acid sequence of a protein, this calculator will provide its theoretical average molecular weight. However, remember that this calculation excludes any post-translational modifications, which are common in mature proteins and can significantly alter their mass.
What if my sequence contains a character other than a valid amino acid code?
The calculator will display an error message indicating an invalid character. You must correct the sequence to include only valid one-letter amino acid codes before proceeding with the calculation.
Is the molecular weight calculated here the same as the mass used in SDS-PAGE?
No, SDS-PAGE estimates molecular weight based on migration through a gel matrix under an electric field, which is influenced by factors beyond just mass, such as shape and charge. While related, the calculated molecular weight from sequence is a theoretical value, whereas SDS-PAGE provides an experimental estimate.
Related Tools and Internal Resources
Peptide CalculatorCalculate properties like isoelectric point (pI) and net charge of peptides.
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