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Biochemistry Questions!!
Moiz_6047
#1 Posted : Sunday, June 06, 2021 11:34:45 PM
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Hi, I had some conceptual Biochemistry questions:

1) Is cholesterol the backbone for steroids or is it the other way? Is the backbone the four-ringed structure with a carbonyl + OH group?

2) Why do basic amino acids contain a positive R at pH 7 and acidic amino acids contain a negative R at pH 7? I thought that acidic amino acids were positively charged and basic amino acids negatively charged. How do the charges compare in acidic/basic solution for the backbone vs the r groups?

3)What does it mean to be chiral and have an absolute s configuration?

4)I understand that the primary structure determines the sequence of Amino Acids but what exactly is the "sequence"?

5)Does tertiary structure determine the 3D shape of the protein? What is the "final conformation"?

6)If two Amino acids are linked via a peptide bond they do not have a quaternary structure? If it is more than one polypeptide bond than it is quaternary structure?

7)How is NADH an organic Molecule? (Coenzyme)? I thought that to be organic you needed to have C-H Bonds?

8)A prosthetic group Is a coenzyme bound to an enzyme; does this definition apply to cofactors?

9)Why is Vmax dependant on enzyme concentration but not Km?

10)For competitive enzymes why does increasing the concentration of substrate increase Km and not Vmax? I thought it would be the other (based on the previous question)?

11)Would you recommend knowing the structure of carbohydrates?

12)Does ATP synthase pump 3H+ out for Every ATP Produced? On page 38 what does it mean by "Each NADH through the ETC Pumps 10 H+ into intermembrane? I thought it was only 4H+?

13)Does Beta Oxidation occur in the mitochondrial matrix, and fatty synthesis in the cytoplasm?

14)Is Primary RNA = Primary Transcript?

15)Do snRNPs cause splicing (removing of introns)?

16)If mutations are permanent changes to DNA how can a "backward mutation" cause a shift to the original DNA?
INSTR_Katie_127
#2 Posted : Sunday, June 13, 2021 2:46:28 PM
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Hi!

1. Cholesterol is the backbone of steroids. Cholesterol is a four-ring structure, therefore the backbone of steroids is a four-ring structure.

2. Lysine, histidine and arginine are the basic amino acids. Bases are proton acceptors, and at neutral pH these amino acids accept a proton onto their R-group NH2 component, which leads to NH3+, making the amino acid positively charged. Conversely, acid amino acids are proton donors, and at neutral pH they kick off their extra proton (COOH becomes COO-), which makes the amino acid negatively charged.

3. Chiral: a molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes (your hands are mirror images of each other but cannot be superimposed onto each other (ie if you attached your right hand to your left wrist it would not look the same as normal)). The Cahn-Ingold-Prelog system is a set of rules that defines the stereochemical configuration of any stereocenter, using the'R ' (from the Latin rectus, meaning right-handed) or ' S ' (from the Latin sinister, meaning left-handed). Each branch of the molecule gets assigned a priority from 1-4, and the number order determines if it is S or R.

4.The sequence of amino acids is the order in which the amino acids are bonded one after the other. For example, the order could be proline-arginine-histidine-etc. That sequence is required to make a protein (insulin for example), while a change in that sequence (ie, proline-aspartic acid-histidine) will make a different protein (glucagon, for example).

5. Yes, the tertiary structure refers to the 3-D shape of a protein. A protein's final conformation is the shape it has to be in to function properly.

6. Peptide bonds are between amino acids, and these are created in the primary structure of the protein. A polypetide refers to a chain of multiple amino acids bonded together via peptide bonds. A quaternary structure is made up of two proteins bonded by hydrogen bonds, Van der Waal forces and ionic bonds.

7. The structure of NADH contains many carbon-hydrogen bonds.

8. I am not totally sure what you are asking here, could you clarify?

9. Km is the amount of substrate needed to achieve half the Vmax. Therefore, it is independent of the enzyme concentration, because it is only dealing with substrate concentrations. Vmax is dependent of enzyme concentration because Vmax is the level at which the enzymes become saturated. If you have a higher enzyme concentration, then there is a higher number of enzymes to be saturated and Vmax will be higher.

10. As I said above, Km is the amount of substrate needed to achieve half the Vmax. Therefore, if you increase the concentration of the substrate, you are increasing the Km. Vmax is dependent on the enzyme concentration, and would not be affected by the amount of substrate added in competitive inhibition.

11. Yes

12. I will pose this question to the instructor in our next BioBiochem session

13. Yes and yes

14. Yes

15. Yes, snRNPs are enzymes that catalyze splicing.

16. A backward mutation is a change from a mutant to wild-type. A "permanent change" means that the mutation cannot be reverse, but it can be mutated again, as we see in backward mutation.

Hope that helps!

Katie (specialist moderator)
Moiz_6047
#3 Posted : Friday, June 18, 2021 1:33:04 AM
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Thanks! Interested in the answer for 12!
Moiz_6047
#4 Posted : Friday, June 18, 2021 1:34:22 AM
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Thanks! Interested in the answer for 12!
INSTR_Kennedy_135
#5 Posted : Monday, July 12, 2021 4:38:27 PM
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Hello Moiz,

ATP synthase allows protons to FLOW down their gradient into the mitochondria. While electrons from NADH are responsible for providing the energy for the PUMPING of protons out of the matrix and it is roughly 10 protons pumped for every ATP. While every NADH makes roughly 3 ATP. Note: I say roughly because there are differences in efficiencies that can happen and you can get fewer ATP than that per NADH. The MCAT goes with 36ATP/glucose while many undergraduate classes are now teaching 32. Go with 36 for the MCAT.

This was confirmed with Torah.

Goodluck!

Kennedy
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