Biochemistry-Official

Biophysics major currently getting a PhD in biochemistry, member of the #officialfam - a group of educational blogs that totally stole @nasa-official's whole thing. Make sure to check out @astrophysics-official, @chemistry-official, and @physics-official when you get the chance!

[sheeplocked]

secondary structure

[biochemistry-official]

What a cool gif! This shows a chain of amino acids folding up into an alpha-helix, a common structure in proteins. I’ll have to make a post soon on the different levels of protein structure!

[scienceprofessorquotes]

However serious and professional you think academia is, subtract a bunch. No, more than that. Even more than that. There you go. I have learned one thing in my life, and that is that academia is not as serious and no bullshit as you thought.

Anon (via scienceprofessorquotes)

[biochemistry-official]

The Central Dogma

What is it? The central dogma is a common way to refer to one of the most fundamental concepts in biology: how organisms store, transmit, and act upon information. It was coined by Francis Crick partially because he forgot the meaning of the word 'dogma.' (Really, he did).  Basically it goes like this:

Image Credit: Khan Academy, “Intro to gene expression”

Long term storage of information (like how to build a protein, or how often a cell should divide) is stored in DNA. When the cell needs that information, the DNA is transcribed into messenger RNA, or mRNA. Then, that mRNA is translated into a chain of amino acids, which folds into a protein that can do work within the cell. It could perform a chemical reaction, become part of a cellular structure, regulate transcription of specific genes, etc.

The DNA to RNA transition is called transcription because the mRNA is basically a copy of the DNA but with a slightly different molecule. It's pretty easy to look at an RNA sequence and figure out what portion of the DNA it was transcribed from. The RNA to protein transition is called translation because it's like the RNA is being translated into a completely different language. Every three bases of RNA (a codon) codes for a specific amino acid. But, since there are 64 possible combinations of RNA bases and only 20 amino acids, there is a lot of redundancy. If you know the exact sequence of amino acids in a protein, you can't figure out the exact RNA sequence that created it.

What are the exceptions to it? Although broad, simple theories are appealing, they almost never capture the true complexity of life. The central dogma is true for most processes in the cell. Genes make RNA, which makes protein. However, there are some exceptions.

Viruses lack the ability to replicate or reproduce by themselves, so they have to infect other cells to survive. Some viruses don't have a genome made of DNA, they have an RNA genome instead. One class of these is called retroviruses, because they move backwards against the usual flow of information described by the central dogma. When they invade the cell, they reverse transcribe their RNA genome into DNA, which gets inserted into the genome of the host. HIV (human immunodeficiency virus) is an example of a retrovirus.

Prions are another example of a process that defies the central dogma. They are proteins that can cause disease by triggering other proteins to switch into a misfolded state. They are infectious, but they don't have any RNA or DNA genomes, they're just a single protein. The first prion discovered was called Prion Protein, because scientists are very creative. Many animals have genes for prion proteins and have tons of normal, healthy prion protein in their bodies. However, these proteins can change shape (misfold) into an alternate, infectious state. Once one protein misfolds, it gets all the other prion protein around it to misfold as well. They clump up into giant, stable aggregates of proteins, which end up killing the cell they're in. Then, the prions find other cells to infect and kill. So, they act like pathogens, but they don't have any genome and don't even fit the definition of a living thing. Examples of prion diseases include mad cow disease, Creutzfeldt-Jakob disease, kuru, and possibly Alzheimer's (the research on this is still pretty new). There are no current treatments for prion diseases, but fortunately they are pretty rare.

[academihahaha]

[biochemistry-official]

How did DNA and amino acids arise? Where did the genetic code come from?

Hi! Thank you for your question. It’s a big one! I can’t answer it definitively because there’s still a lot to learn about how the chemistry of life began. However, the prevailing theory right now is called the RNA World.RNA is a nucleic acid very similar to DNA, with almost the same set of nucleotide bases. RNA uses adenine, uracil, guanine, and cytosine while DNA uses adenine, thymine, guanine, and cytosine. RNA also has one extra hydroxyl (an oxygen bonded to a hydrogen) group than DNA, so it is slightly less stable. In cells, RNA is more commonly found in short, single-chain strands and DNA is found in long, double-chain helices (your genes!).But the interesting thing about RNA is how it folds. Since it doesn’t have a complementary strand like most DNA, it binds to itself in very interesting shapes. Here’s an example of how a strand of RNA binds to itself - the first image shows which base pairs interact, and the second shows the three-dimensional shape formed. Here’s a link to the paper it’s from.

These folds are very interesting because they can actually act like enzymes, which we normally think of as complicated molecules made out of twenty different amino acids. But RNA enzymes (which we call ribozymes, from ribonucleic acid + enzyme) can do crucial chemical work despite only being made of four bases. Ribozymes are a huge component of ribosomes - the molecular machine responsible for translating genetic information into proteins.So the prevailing theory is that - since RNA can both store information (like DNA) and act on that information (like proteins) - the first form of life was simply self-replicating chains of RNA. Over time, these chains became more complex and developed into the DNA/RNA/protein system most life uses today (viruses and prions are potential exceptions, but may technically not be ‘alive’). DNA is much better at storing information than RNA, and proteins are more versatile for chemical work than RNA, which is probably why we don’t see self-sufficient RNA life-forms today (or we just haven’t discovered them yet! The world is a big place). Thanks again for the question!

[biochemistry-official]

So I could probably watch this video forever, because it looks like How It’s Made, but for DNA instead of rollerskates or something. The full video is by the Walter and Eliza Hall Institute of Medical Research. Explanation of what’s happening is below the cut.

Keep reading

[biochemistry-official]

Size doesn’t matter

Since genomes are basically instruction books for making organisms, you’d think that complicated organisms (like people) would have larger genomes than other organisms (like plants and simple animals). But it turns out that isn’t necessarily true! Human beings have roughly 3.2 billion base pairs in our genome, which is about 3.3 Gb of data in every cell. That’s a lot! But it’s nowhere close to the vertebrate with the largest genome: Protopterus aethiopicus, or the marbled lungfish. 

The lungfish has 130 billion base pairs in its genome. Look at that smug face. But she’s still pretty far from the largest confirmed genome. So far, the biggest one that has been found belongs to an organism called Paris japonica.

That’s right, it’s a plant. It’s genome is 150 billion base pairs, which is frankly ridiculous. This is partly because, while animals have pretty strict rules about chromosome numbers, plants don’t really care as much. Paris japonica’s genome is probably allopolyploid - meaning it contains duplicate chromosomes from multiple species. Researchers suspect it is a hybrid of four different species!

[topshotpicks]

[youthoughtiwasasleepdidntyou]

I feel these in my soul

[twisteddoodles]

Science

[popsci]

This week scientists announced something kind of weird: Using the gene editing technique CRISPR, they encoded a series of images and a GIF into the DNA of E. Coli. Scientists have actually been encoding images and basic pieces of information into bacteria for years. But encoding a movie represents a big storage upgrade.

Read more

[biochemistry-official]

Using bacteria to store information is a really interesting idea, and a testament to how efficient and accurate gene editing is becoming with the help of CRISPR. 

[twisteddoodles]

Antibiotics

[biochemistry-official]

This is a great way to remember that antibiotics do not treat viral infections! This includes colds and the flu. Unfortunately, there are not very many anti-viral medications that actually work.

[astrophysics-official]

can we start a book recommendation thread because i need new books to read this summer!! i like sci-fi a lot but i’m up for literally anything. I’ll start:

Jurassic Park, Michael Chrichton

tbh anything by Michael Chrichton

Dragon’s Egg, Robert Forward

this book isn’t available in bookstores but you can find it online

Silence of the Lambs, Thomas Harris

also! thriftbooks.com is a fantastic resource to get these books for MUCH cheaper than your local bookstore!!

[biochemistry-official]

Here’s what I could come up with off the top of my head! All books I would highly recommend to most people.

 • The Cormoran Strike series by Robert Galbraith (actually J.K. Rowling). A grumpy, ex-military private detective with one leg and a heart of gold solves murders with his secretary/assistant/fellow detective (by the third book) Robin Ellacot. They’re very well written! The third book is the scariest book I’ve ever read.

• The Martian by Andy Weir.  Deserved all the hype it got, funny and fascinating. Better than the movie.

• 11/22/63 by Stephen King.  An English teacher discovers a portal back in time to 1958 and decides to stop the assassination of JFK. A lot of other stuff happens. An accurate-to-the-time-period thriller with some sci-fi thrown in.

• The Moon is a Harsh Mistress by Robert Heinlein. This is a relatively old sci-fi book, but it’s fantastic. It occurs in a future where a prison colony established on the Moon becomes permanent (because people who lived for a long time have trouble adapting to Earth’s gravity and can’t come back). It develops a drastically different society from Earth and eventually rebels. There’s also a sentient supercomputer named Mike. I read it a long time ago but I loved it.

• The Gene by Siddhartha Mukherjee. A non-fiction book about the history of genetics. It’s well-written and easy to understand even if you don’t know much about the topic. It also spends a lot of time on the rise and fall of eugenics, which is horrifying but fascinating. There are a lot of lessons that can be taken away from it on how to ensure science is a force for good instead of evil.

[bridgetothephd]

What are great questions to ask to a potential graduate advisor about their research practices, how they run their lab, etc to see how they’re a good fit?

What are some things you wish you knew about your advisor before you selected your program?

[cancerbiophd]

Where do your students end up? (ie. post-doc, academia, industry, etc)

On average how long does a (Masters/PhD) student in your lab take to graduate?

Do you, the PI, do lab work still?

Did any of your students receive fellowships/scholarships/grants that they applied for?

What’s the structure of your lab meetings?

What’s the structure of your individual meetings with students?

Do you travel a lot for conferences?

Do you work from home a lot? (My PI does this a lot and I kinda wish I had known this beforehand, just as a head’s up)

Do you have other responsibilities that remove you from the lab? (ie. if they run a company, do clinical work, teach, etc)

What percentage of your time/resources do you aliquot per project? (Some PIs may spend more time on one project than others)

What are your expectations of students in terms of how long they’re in the lab each day? Do you expect students to work evenings, weekends, and/or holidays?

What are your holiday and sick days policies?

Do you allow students to read papers/do their writing while in lab? (I know one PI in my program who doesn’t allow their students to read papers while in the lab, because lab time is for lab time)

Who will my immediate mentor be in terms of research questions (ie. another graduate student, a post-doc, or the PI themselves)?

Are you familiar with the requirements of my graduate program (ie. committee meeting structures, qualifying exam structure if applicable, how the thesis should be formatted, etc)

This one you may want to ask the current personnel in the lab: Are there any labs/PIs that this current PI isn’t on good terms with? (This is something you may need to know when setting up your committee, for example, or collaborators). 

How do you determine the authorship on papers? (ie. How much work should I do for a project for my name to be on it?)

How many papers do you publish per year? 

How many papers do you expect your graduate students to publish during their time here?

How often do your students go to conferences/present at meetings?

Do you allow your students to have other engagements (like TAing, internships, etc)?

And in general, if you have a huge life event coming up, ask them what the process on that would be. For example, if you’re getting married, or planning on having a child, or have a family member who’s gravely ill, ask them how much time you can take off, etc. If the PI seems really hesitant or put-off by that, that’s something to consider. 

That’s all I can think of.. I’m sure there’s more if anyone else has anything to add. 

Good luck!

[biochemistry-official]

As someone just entering graduate school, this is very useful for me! Hopefully it will be useful for some of you as well.

Thanks @astrophysics-official for putting this on my dash!

[aimingforexcellence]

[biochemistry-official]

Why I hoard pipet tips where no one else will find them (I’m the type on the right).

[standingcowrrdly]

AP Chemistry is a serious subject

[biochemistry-official]

How did DNA and amino acids arise? Where did the genetic code come from?

Hi! Thank you for your question. It’s a big one! I can’t answer it definitively because there’s still a lot to learn about how the chemistry of life began. However, the prevailing theory right now is called the RNA World.RNA is a nucleic acid very similar to DNA, with almost the same set of nucleotide bases. RNA uses adenine, uracil, guanine, and cytosine while DNA uses adenine, thymine, guanine, and cytosine. RNA also has one extra hydroxyl (an oxygen bonded to a hydrogen) group than DNA, so it is slightly less stable. In cells, RNA is more commonly found in short, single-chain strands and DNA is found in long, double-chain helices (your genes!).But the interesting thing about RNA is how it folds. Since it doesn’t have a complementary strand like most DNA, it binds to itself in very interesting shapes. Here’s an example of how a strand of RNA binds to itself - the first image shows which base pairs interact, and the second shows the three-dimensional shape formed. Here’s a link to the paper it’s from.

These folds are very interesting because they can actually act like enzymes, which we normally think of as complicated molecules made out of twenty different amino acids. But RNA enzymes (which we call ribozymes, from ribonucleic acid + enzyme) can do crucial chemical work despite only being made of four bases. Ribozymes are a huge component of ribosomes - the molecular machine responsible for translating genetic information into proteins.So the prevailing theory is that - since RNA can both store information (like DNA) and act on that information (like proteins) - the first form of life was simply self-replicating chains of RNA. Over time, these chains became more complex and developed into the DNA/RNA/protein system most life uses today (viruses and prions are potential exceptions, but may technically not be ‘alive’). DNA is much better at storing information than RNA, and proteins are more versatile for chemical work than RNA, which is probably why we don’t see self-sufficient RNA life-forms today (or we just haven’t discovered them yet! The world is a big place). Thanks again for the question!

[surprise-adoption]

Bottle rocket under ice

[overtheunderpass]

rad 

[edwardspoonhands]

I’m pretty sure that the reason the ice fractured into six slices is the same reason snowflakes are often six sided and it has to do with the shape of a molecule of water and I just think that’s so freaking cool.

[opulene-archive]

How would it even stay lit though?

[orangejuiceaholic-deactivated20]

!!!!! it IS actually because of the structure of water molecules! Water molecules are fuckin weird, as are lots of other liquid substance molecules, because theyre shaped like fuckin HEXAGONS! hexagons are those weird, six-sided shapes that re very sturdy, but they dont tend to sit very well when stacked together. thats why, when you fill up a glass of water to its full capacity, it can go OVER the brim a little and not spill over. It’s also why water beads.

anyway, so since water is essentially made up of a gazillion little hexagons, it tends to gather into larger hexagons as it shapes together. this is not visible unless the water is in a solid form, aka ice. when the water is split, it tends to crack around the established hexagons. that bottle rocket exploded in the PERFECT place to show this phenomenon and its geeking me out.

ALSO! the bottle rocket stays lit because the fuse was definitely waterproof and made with magnesium and an oxidizer of some sort. this means that they will burn underwater because they dont need the oxygen from the air to stay lit. thats so fucking weird isnt it. im tipsy and its the 4th of july. sorry for the science haha

[inside-us-only-stars]

Don’t you dare apologize for science

[biochemistry-official]

Water molecules actually aren’t hexagonal themselves, but they form hexagonal crystals when they freeze! This is because the hydrogen atoms have a positive charge and the oxygen atom has a negative charge, so a hydrogen on one water molecule is attracted to the oxygen on another water molecule. This difference in charge across a molecule is called a dipole.

This hexagonal crystal shape is the lowest energy organization, so it forms at low temperatures and creates solid ice. In the image above the black lines are covalent bonds (electron sharing, very strong) and the white ones are polar bonds (positive/negative attraction, not very strong). The red circles represent oxygen atoms and the blue circles represent hydrogen atoms. The reason water can stay above the brim of a glass isn’t necessarily because of the shape of the water molecules, but again because of the different charges on different parts of the molecule. In liquid form, water molecules make very brief associations with each other as they move around. They are constantly switching polar bonds from one neighboring molecule to another, forming very short-lived tetrahedral (four-sided pyramid) shapes. Even though they are moving, this creates surface tension - a force that ‘holds’ the water together. For small amounts of water, like the amount above the brim of a glass or in a drop of water, this is strong enough to oppose the other forces acting on it (like gravity). Water has a lot of unique properties because it’s polar! The hexagonal organization of ice makes it less dense than liquid water, so it floats to the top and insulates the rest of a lake or pond from the cold. This prevents it from freezing solid, which is very important for aquatic animals. It’s also very good at dissolving ionic compounds like salt, and has a high specific heat which means it can absorb a lot of heat without it’s temperature increasing very much. If water didn’t have these properties, life might not have evolved on Earth, because cells rely on these properties to function. That’s one commonality between all life on Earth - requiring water. So that’s pretty neat!