/r/Biochemistry

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A place to post news and discuss the frontiers of biochemistry and biotechnology. Please refrain from posting home videos with songs and raps.

/r/Biochemistry

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1

Biochemistry: [2,3-13C2]lactate to glucose

Can someone please help me?

I know the tracking of radiolabeled carbons from glucose to lactose but I am having trouble with the opposite.

What kinds of glucose isotopomers are expected through hepatic gluconeogenesis after [2,3-13C2]lactate administration? Please include a brief diagram to show metabolic pathways from lactate to glucose.

I know the carbons in position 2 and 3 remain after lactose is converted into pyruvate and then the carbon in position 3 is lost once pyruvate is converted into oxalacetate but I am confused on the fate of the carbons after (conversion to PEP, DHAP-GA3P, Glucose) , what ends up being labeled in glucose?

Thanks in advanced!

4 Comments
2024/02/12
02:53 UTC

34

In the real world, diluting a buffer does change the pH, and not necessarily approaching 7.0. What is the real-world answer?

Hello fellow biochemists. I am a biochemistry professor and researcher, and I feel like an absolute idiot because this real-world problem is stumping me.

In the "ideal" world of undergraduate biochemistry and chemistry textbooks, we tell our students that diluting buffers should a) not change the pH, or b) in cases of extreme dilution, the pH approaches that of pure water, namely 7.0. The argument for answer b is that the concentration of the acidic and basic forms of the buffering molecules can be diluted to insignificant concentrations compared to water, thus the pH approaches 7.0. The argument for answer a, is that as we dilute, the acidic and basic forms of the buffering molecules change with equal proportions, but remain constant relative to each other, thus according to the Hendersen-Hasselbalch equation the pH remains the same.

Now, let's put all of that "ideal" stuff aside for the moment. In the real world, it apparently isn't that simple.

A very well-known example is the preparation of phosphate-buffered saline (PBS). There are numerous documents and internet pages detailing the recipe for preparing a concentrated stock and a working solution of PBS. In many instances, these protocols state that 10x PBS has a pH closer to ~6.8, and that upon dilution to a 1x working solution, the pH shifts to ~7.4.

I encountered a similar phenomenon in my own work this week. I personally prepared a series of 10x phosphate buffers (no saline) using monobasic and dibasic sodium phosphate salts. These 10x phosphate buffers were prepared at incremental concentrations, i.e. 7.0, 7.2, 7.4, 7.6, 7.8, 8.0.. I used a calibrated pH meter to prepare each of these 10x phosphate buffers. However, when I diluted them to 1x concentrations, their pH seemingly increased significantly. For instance, the 10x stock of the pH 7.4 buffer rose to pH 7.9 upon dilution to 1x, and the 10x stock of the pH 7.8 buffer rose to pH 8.2 upon dilution to 1x. These increases of 0.5-0.6 pH units would seem to be in line with the aforementioned example of PBS dilutions from 10x to 1x.

I would really love to know the real-world rationale for why this is happening. Internet searches don't seem to yield consistent explanations, other than something to the effect of... dilution changes ionic strength, and ionic strength afects acid ionization.

Anyone have any thoughts? Thanks in advance!

16 Comments
2024/02/11
15:12 UTC

8

Postgrad help

Hello! I’m a third year undergrad biochem student and I’m kinda lost on what to do after I graduate.

I was thinking of doing a masters in biomedical science but I’m worried that there could be more interesting options that I don’t know about.

I love what I’m studying but my GPA is slightly lower than the minimum GPA required for a masters, so will working a lab job help me get into grad school since experience will be taken into consideration rather than my undergrad grades?

I hope I don’t get judged too much for this question! My advisor isn’t really helping and I have no one else to ask.

Thanks in advance! :)

6 Comments
2024/02/11
00:21 UTC

5

Is having two PI's in grad school a good idea?

Just went to a grad school visit for chemistry. There's two professors there in the same division (bioanalytical) who do research that has the potential to be complementary and they have apparently talked about collaborating before. One is currently up for tenure and will most likely get it, while the other just started in August.

If I had to choose I'd go with the tenure one, but I really like both research groups. Can I ask for a Co-PI situation? Are there any issues that could come up with having two PI's?

13 Comments
2024/02/10
18:56 UTC

14

Drug design - help with major

hi, im a molecular biologist but would like to get a masters (and later phd) in organic chemistry, biochem, medicinal chemistry, or bioinformatics. I’d like to work in drug design in the future (designing molecules based on receptor shape, wanted properties etc), my thesis was neurochemistry related.

which of these do you think will give me the best education to go that path? and if you majored in either of those what other jobs in the industry do you work in? I primarily wanted to stay in elementary research in academia but I’m not so sure with the pay, so sth as close to that would be ideal.

(cross posting)

6 Comments
2024/02/10
14:22 UTC

3

What's the best textbook for cinical biochemistry?

how's Biochemistry with Clinical Correlations with Devlin?

1 Comment
2024/02/10
07:42 UTC

6

Any shot of working remote with a Biochem bachelor or master?

I want to get my bachelor in biochemistry. Im working part time in a lab right now and it's great, but I have health problems and I don't think lab work is a sustainable future for me anymore.

I was gravitating towards research or project leadership in the field anyways, but I want to be more sure that I'll have options before it's too late for me to switch to IT which almost guarantees remote.

Any advice?

11 Comments
2024/02/10
06:01 UTC

2

Feb 10: Cool Papers

Have you read a cool paper recently that you want to discuss?

Do you have a paper that's been in your in your "to read" pile that you think other people might be interested in?

Have you recently published something you want to brag on?

Share them here and get the discussion started!

0 Comments
2024/02/10
01:00 UTC

1

Recombinant proteins

Hello! I want your help! I have ocd and hiv fears!

Can recombinant antigens and proteins from a test HIV kit cause inflection if someone touches them with an open bleeding wound before doing the test and after? I fear that i transfer with my hand these antigens in my house on towels while i touch the membrane of the test and then i touch a towel and if these antigens stay on towel and my familys members use this towel to clear an open wound or if i touch this membrane with my pricked finger while i try to do the test and come into my blood stream. I ask my doc and told me that these antigens are not contagious but i need more opinions

1 Comment
2024/02/09
19:23 UTC

11

How can you finish studying biochemistry in two days and a half?

I have a biochemistry final exam on Monday, a total of 7 chapters with an average of 150 slides each. although I've studied them all (except the last) and did well on quizzes, I feel like I'm so overwhelmed with the amount of things the I have to study, I feel like I've forgotten everything and there's no enough time, I need at least one day for each in order to finish it perfectly and understand everything as I should (as you know biochemistry has lots of details).

what makes things worse is my anxiety, I keep getting anxious and I'm unable to actually focus and study because I'm so worried about the time running out, this happened with me in the molecular biology course the previous semester and I did horrible, I fear this will happen again now.

any tips on how can I finish all of this in 2 days??

I finished one chapter yesterday and have 6 left, have been studying another one today but I'm not really productive or proceeding.

14 Comments
2024/02/09
15:54 UTC

16

Double Major or Three Years?

Title.

Due to my amount of AP credits I have, if I only major in Biochemistry I have to graduate in 3 years. I was thinking that I could double in Microbiology, which has some overlap but would add enough course load so I could graduate in 4. I'm in a really privileged position as to not worry about tuition costs and as I'm going to a large research university, I want to use the resources here to their fullest advantage.

Would it be worth it to double major and stay another year here, hopefully gaining more research experience, or should I graduate early and move on to graduate school?

12 Comments
2024/02/08
18:10 UTC

6

I'm lost

Hi. I'm a medicine student but i'm terrible with math, physics and i only know the basics on chemestry, actually. I'm know struggling to understand enzymatic kinetics but all those equations don't seem to make any sense for me. I've tried reading it on the Lehninger first but i wasn't understanding a thing, then i watched videos thinking it would make it easier for me, but the only thing that can get into my mind is that Km is equal to the [S] in the moment where the velocity is half of the Vmax or that Vmax is when all the active sites of the enzyme are occupied.
There is something that i should learn before to properly understand this stuff? I mean, i have not been facing any problems with the first pages of the chapter of Enzymes before this.

8 Comments
2024/02/08
17:56 UTC

6

Effect on enzymatic affinity on increasing enzyme concentration.

Increasing enzyme concentration increases the Vmax for a given enzyme-substrate system, so naturally, the new Vmax/2 is also more than the previous one.

But as per the literature, Km for the new scenario is the same as the previous Km (before increment in enzyme conc) that means amount of substrate required to reach the new increased Vmax/2 is same as it was before (required to reach old Vmax/2). So if by using the same amount of substrate we can now achieve more speed (new Vmax/2) isn't the affinity increased? But isn't Km an indicator of affinity of an enzyme and it remains a constant? So is there any change in affinity or not?

5 Comments
2024/02/08
07:31 UTC

17

I don’t know what to do during biochem lectures

Idk what to do, if I focus on note taking I miss out on the info and if I focus on the lecture I forget, if I write down important parts only my notes don’t have a logical flow

Please please please help.

18 Comments
2024/02/08
06:57 UTC

6

Book recommendation to study immunology

Hello everyone, I'm studying biochemistry and I love immunology a lot, buy I know that what I know about the subject is not a lot, and I'd like to learn more, so, if you have any recommendations, I'd be glad to read them. I speak Spanish, though, and sometimes I have trouble understanding English cientific language, so if the books that you suggest are translated onto Spanish I'd be really happy. Thank you so much!!

4 Comments
2024/02/07
23:58 UTC

18

How do you keep up with the latest papers in your field?

What sources do you go to or how do you find out about them? I'm not the biggest fan of pubmed, so I'm looking for alternatives

14 Comments
2024/02/07
19:30 UTC

2

Feb 07: Education & Career Questions

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

2 Comments
2024/02/07
16:00 UTC

0

What goes on during incubation period?

I am curious if the incubation period is determined by the ability of the virus to evade the immune system. Specifically thinking about the role the mitochondria plays in the immune response and how viruses like to attack it.

3 Comments
2024/02/07
02:46 UTC

22

Is biochemistry more chemistry or biology?

Hey guys,

I'm a community college student working on a 2+2 program. I chose the biochem path honestly because it sounded cool (my advisor was pressuring me to decide a path quickly and not much thought went into it). I'm a freshman, so i've taken gen chem and bio 1, among a few other classes. I enjoyed Gen bio 1, it was all cellular and molecular biology. However, I hate gen bio 2. It's all animals and morphology, it's honestly such a drag. I'm now reconsidering my decision to pursue BioChem. I much prefer chemistry and I'm considering switching my path to strictly chemistry.

Any advice would be great.

36 Comments
2024/02/06
22:57 UTC

4

How relevant does your undergrad research need to be for a biochemistry PhD program?

I'm currently in a neuroimmunology lab. There are techniques that overlap, but it's not exactly biochemistry. I have been considering doing a PhD in biochemistry (my major) lately, but definitely not sure about a specific direction or research question as I don't have much experience in my coursework yet.

Should I try to get research experience as well in a specifically biochemistry lab/internship program/REU before applying? Would it be a red flag to apply with loosely relevant research skills?

13 Comments
2024/02/06
22:18 UTC

3

Need help getting prepared!

Hey everyone!

This fall I’ll be starting a biochem - premed program, but there is one small problem. I’ve been out of school for eight years.

What would be the best way for me to spend the next 6 months “catching up” on the material that I should already know.

I’m mostly concerned about Calculus as my highest math was pre algebra ( wasn’t the best kid in high school)

Any tips would be greatly appreciated!

5 Comments
2024/02/06
21:47 UTC

12

Is there any relation between the Krebs cycle and menstruation?

As title implies, my professor left me with said question to ponder on. But, in all honesty, I fail to see the relation?

Am I not looking further enough? Please, I would like some insight.

14 Comments
2024/02/06
21:13 UTC

3

ASBMB accreditation exam

Hello hello, I was wondering if anyone has recently (past 5 years) taken the ASBMB accreditation exam? They have a few practice questions on their site, but I was wondering if people had any good tips for how to study and how it went on test day?

1 Comment
2024/02/06
21:09 UTC

4

isoelectric point prediction and tertiary structure of proteins

Hey, I was wondering how accurate IP predictions based on protein sequences are.

Pretty high, I would guess, but I am not shure if the tertiary structure has any influence on it. Does it make a difference wether certain amino acids are on the outside and exposed or inside the protein?

9 Comments
2024/02/06
17:46 UTC

2

What is the best extra celullar matrix option for tissue engineering?

I am making a thesis regarding this topic so I wanted to hear suggestions. The best choices I've seen are synthetic and porcine intestinal submucosa. What's the most cost reduced choice out there with best biological compatibility?

7 Comments
2024/02/06
12:05 UTC

8

Help to remember the amino acids

I need to remember the names, structures, polarity of all 20 amino acids. Any tips and tricks or even mnemonics will help please and thank you

16 Comments
2024/02/06
03:14 UTC

1

Can someone help me understand this article and implications re: minoxidil and estradiol?

Hi all,

Well first, I hope what I'm going to post- which is essentially asking for help- isn't inappropriate. Also, I don't know if I've used the right flair, so I'm sorry if I haven't... I'm a 58-year old (young!) woman with very early stage estrogen-receptor positive breast cancer. I also, unfortunately have thinning hair and for that I started using topical 5% minoxidil foam in Aug 2023. My oncologist says this is fine, and I see that Memorial Sloan Kettering ( a premier cancer center) also endorses use of minoxidil for women like me. However, I can find not a single study showing safety in breast cancer patients. The prevailing view is that minox is primarily a vasodilator, but I came across this study (linked below). I don't have the background to truly understand all of it, but it seems to say that minoxidil increases estradiol (though is this peripheral or systemic? how do the amounts in the paper for control vs minox increases translate to systemic levels?) I don't understand the gene transcription information about CYP19A1 or what the implications are of the fact that there was no difference in protein expression. I'm on an aromatase inhibitor, which blocks the conversion of androgens into estrogens. My interpretation of this article is that minoxidil is doing the exact opposite and I fear that I shouldn't be using it at all. I'm very much in a bind because losing much of my hair- it's so awful for a woman- but if it's increasing my risk of a cancer recurrence I want to know.

Thank you in advance-p.s. this isn't a homework assignment :)

https://pubmed.ncbi.nlm.nih.gov/37645625/

0 Comments
2024/02/05
21:48 UTC

3

Conceptual Question

Hey! I've taken a bunch of chemistry and biochemistry courses but I've always had a question that I never bothered asking: Why is it that steroids must have 4 fused rings? What is it about 4 rings that gives them a special nature as opposed to 3 rings?

11 Comments
2024/02/05
18:40 UTC

3

Feb 05: Weekly Research Plans

Writing a paper?

Re-running an experiment for the 18th time hoping you finally get results?

Analyzing some really cool data?

Start off your week by sharing your plans with the rest of us. å

1 Comment
2024/02/05
16:00 UTC

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