@spellbiomentors - Tumblr Blog

Why do we get hot when we run?

Our metabolism is not 100% efficient, so when we burn glucose, some of the energy in its bonds is released as heat instead of transferred (through the elaborate process of glycooysis and/or respiration) to bonds of ATP. The more fuel we burn (and the more ATP we burn), the more heat is given off.

What are the evidences supporting the hypothesis that glycolysis is an ancient metabolic pathway?

It is found in all organisms, suggesting that it appeared early on in evolution. At that time, the earth had no oxygen. Only when oxygen increased in the earth's atmosphere (due to photosynthesis) was aerobic respiration possible.

hydrogeneportfolio

Minimal Posters - Six Women Who Changed Science. And The World.

How exactly is one strand of DNA able to be both leading and lagging? Do we determine that from the origin of replication?

When the strands are separated at the "origin", the new DNA can be made only in one direction on one strand towards the fork. After a little more has opened, lagging strand synthesis can start on the other half of the replication fork. Thus, a replication fork has both leading and lagging strand synthesis, and each template strand is being copied (on different sides of the bubble) by leading and lagging synthesis at the same time.

Pictures are worth a thousand words.

how is the structure of peroxisomes related to their function?

Peroxisomes are packed with the enzyme catalase to break down hydrogen peroxide created from redox reactions. There are so many of these enzymes that they form a crystalline structure in the organelle.

which organelles are part of the endomembrane system?

Everything but peroxisomes, mitochondria, and chloroplasts. Those organelles make their membranes independent of the endomembrane system. The proteins that end up in them are directed to them by a mechanism other than the protein processing pathway of the endomembrane system (rough ER, Golgi, and vesicles).

do we need to know the things you put on the board but that we didn't get to in class? such as somatic mutation, germline mutation, types of mutations (silent, synonymous, non-synonymous, missense, nonsense, frameshift), photoreactivation/photolyase, and Ames test?

Yes for somatic mutation, germline mutation and photoreactivation/photolyase

during G1 phase, are the organelles replicated too?

in G1 and G2

Not as much a question as a reminder. All the BioMentors and TAs for this class, thank you so much for everything that you all do. I just want to remind every single one of you how thankful I and so many other Intro Bio students are for all of the time you put in to answer our questions and calm our biology woes.

You are very sweet! Thank you for keeping us motivated to help you learn biology!

How are radioactive isotopes used to trace and identify biological molecules?

A molecule is labeled only if that molecule contains an radioactive atom. Proteins could be labeled with radioactive H, C, N, or S. Nucleic acids could be labeled with radioactive H, C, or P. Don't memorize this list: if you know the structure of a biomolecule, you can predict whether it would be labeled using different isotopes.

Sometimes, we get the radioactivity in the cell by feeding the cells radioactive isotope. Any molecule that the cell then synthesizes will then contain those isotopes and be labeled. Sometimes, we synthesize a radioactive molecule in the lab then add it to the cells or cell culture.

We just did this in class to follow the processing of newly made proteins in a secretory cell or the synthesis of nucleic acids to follow the cell cycle. The radioactivity was incredibly useful because it helps us be able to know where the molecules are located. A specialized experiment is a pulse/chase experiment where you add radioactive molecules for a short period, then wash it out. By following the radioactivity, you can watch how a molecule moves through the cell.

Does tertiary structure form before secondary? I ask because it appears as if the only way the polarized backbones would come together is if they were forced together by some other interaction (between R groups perhaps) that brought them in close contact, rather than doing so spontaneously.

There is no schedule for interactions. Whatever happens first will affect the possible interactions. So your idea about the need for R group interactions in order to facilitate secondary structure is very possible.

What does this mean: "Be able to recognize and predict the effects of multiple hydrogen bonds on the behavior of biological molecules."

Let me answer your question with a question. Why is cellulose so strong? How would having a high percentage of G's and C's affect the strength of double stranded DNA? How do sequoia redwoods get water up to the very top? How do geckos walk on walls? I hope you get my drift...

Why are the ends of nucleic acids are called 5’ and 3’?

A strand of nucleic acid is a string of nucleotide monomers. On one end of the string is the free (unattached) phosphate group, which is attached to the 5'carbon of the sugar. On the other end of the string is a free hydroxyl group attached to the 3' carbon of the sugar. 5' and 3' is a short-hand way to describe the two ends. Double stranded nucleic acids are arranged in a anti-parallel way:

5'--3'

3'--5'

What is the difference between a nucleotide and a nucleoside?

A nucleoside refers to just the sugar (ribose or deoxyribose) and the nitrogenous base (A, T/U, C, G).

A nucleotide refers to the sugar, base, and phosphate group(s).

So, for example, a nucleoside triphosphate is a form of nucleotide.

Do hydrogen bonds necessarily have to be polar?

I think you're mixing up a few ideas here.

Hydrogen bonds are not polar because they are not really bonds, but more like electrostatic interactions.

Hydrogen bonds occur between two atoms that are both in polar bonds.

When a molecule contains many atoms that are capable of making hydrogen bonds, the molecular is considered "polar" and is water soluble.

ok, three questions: 1. Do we need to know about denaturing of proteins and the effects that has on structure? 2. What effect does being in an aqueous solution have on different bonds? 3. Do we need to know/what is the difference between saturated and unsaturated fats? Thank you for doing this!

I’m not the authority on this, as the test will be made by Dr. Spell, but it’s late and I will do what I can to set your mind at ease.

1. You should know as much as you need to explain what we did in class. We talked about how a pH change affects protein structure when we discussed hemoglobin’s oxygen binding affinity. Don’t worry too much about the mechanism, but be sure to brush up on interpreting graphs, equilibrium of reactions, etc.

2. I’m not sure what you mean by this. Are you talking about solubility? If so you should definitely be able to explain that.

3. We have not talked about this yet, so don’t worry. When we do it will be in the context of cell membranes and how their permeability is affected by “kinks” (double bonds) in the hydrocarbon chains.

From Dr. Spell:

Good answers. Here is what I would add:

My first Tumblr post!

1. To “denature” means to remove the inherent nature of something. The “nature” (i.e. structure) of proteins is determined by the kinds of interactions it has. Changes in pH can change the ability of the protein to hydrogen bond or ionic bond with itself (due to competition from all of those H+’s). Raising the temperature can cause those hydrogen bond sand van der Waals to fall apart. Changes in these interactions will change the shape; changes in shape can change the function. Hemoglobin was a good example of this.

2.Ionic bonds are very strong,except in water (due to competition from all those partial charges of the water).

3.Coming soon!

ORIGINAL POST

Thanks for the submission! Yes, I just saw it on the news too. To be honest I'm too worried after what Dr. Kraft said today. I never thought I would comforted by diarrhea...

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