Estimating Volumes of Amino Acids in nm^3

In summary, the conversation suggests estimating the volumes of various amino acids in units of nm^3 by considering a combination of bond length and atomic radii, as well as calculating the volume of individual atoms and fitting them into 3-D shapes. It is noted that treating amino acids as spheres may not work for all cases. The accuracy may be compromised due to overlapping electron orbitals. The group also discusses the potential for using a more creative approach rather than aiming for an exact answer.
  • #1
Krazer101
18
0

Homework Statement


Estimate the volumes of the various amino acids in units of nm^3


Homework Equations


V = 4/3*pi*r^3


The Attempt at a Solution


Is it alright to treat the amino acids as spheres? Using this I was thinking of measuring the distance, atomic radii and bond length, between end of R group and C terminus. Is this the right way to go or am I missing the problem completely?
 
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  • #2
Assumption about spheres won't hold. But I think you are right that some combination of bond length and atomic radii is the way to go. My guess is that nobody expects exact answer, you are just expected to be creative and find a reasonable way of finding the answer that will be in a correct ballpark.
 
  • #3
I'd just calculate the volume of the individual atoms and add them up
It won't be very accurate (because of overlapping electron orbitals) but I don't think its meant to be

hint:watch out for hydrogen
 
  • #4
That was my first thought, I just decided to not post it :tongue2:
 
  • #5
I was thinking along the lines of that too, but I was just wondering if there was a better solution. The book solved many of the estimation problems by fitting the molecule, atom, etc into a 3-D shape, so I was thinking along those lines. Thank you for the help though, its much appreciated.
 
  • #6
Fitting into 3-D shape is a good idea, but sphere won't work for all amino acids - for example phenylalanine has rather bulky and flat ring attached.
 

1. How do you estimate the volume of amino acids in nm^3?

To estimate the volume of amino acids in nm^3, you must first determine the number of amino acids present in the sample. This can be done by calculating the molecular weight of the amino acids and dividing the total weight of the sample by the weight of a single amino acid. Next, you can use the known dimensions of a single amino acid molecule to calculate its volume. Finally, multiply the volume of a single amino acid by the number of amino acids present in the sample to estimate the total volume in nm^3.

2. What are the common methods used for estimating volumes of amino acids in nm^3?

The most common methods used for estimating volumes of amino acids in nm^3 include X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and molecular modeling. X-ray crystallography involves analyzing the diffraction patterns of crystals of amino acids to determine their structure and volume. NMR spectroscopy uses the magnetic properties of amino acids to determine their structure and volume. Molecular modeling involves using computer simulations to estimate the volume of amino acids based on their structure and composition.

3. How does the volume of amino acids relate to their function?

The volume of amino acids plays a crucial role in their function within a protein or enzyme. The specific shape and size of an amino acid molecule determine its interactions with other molecules, such as other amino acids, DNA, and enzymes. Additionally, the volume of amino acids can affect the folding and stability of proteins, which is essential for their proper functioning.

4. Can the volume of amino acids vary between different species?

Yes, the volume of amino acids can vary between different species. This variation is due to genetic differences that can result in different amino acid sequences, which can ultimately affect the size and shape of the amino acid molecules. Additionally, environmental factors such as pH and temperature can also impact the volume of amino acids in different species.

5. How accurate are the estimated volumes of amino acids in nm^3?

The accuracy of estimated volumes of amino acids in nm^3 can vary depending on the method used for estimation and the quality of the data. X-ray crystallography and NMR spectroscopy are generally considered to be more accurate than molecular modeling. However, even with these methods, there can be some margin of error due to experimental limitations. It is essential to consider the limitations of each method and the potential sources of error when interpreting the estimated volumes of amino acids.

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