Biochemistry - Blog Posts
What comes to mind when you think of alcohol? Probably alcoholic drinks like beer or wine. But in organic chemistry alcohols are an important and versatile family of compounds. In this episode of Crash Course Organic Chemistry, we’ll use alcohols as a starting point to get other types of compounds like ethers, epoxides, and more!
Biochemistry
Update: Pictures are working!
Atoms
There are a few basic chemistry concepts that are essential to understand. For starters, understanding what an atom is and its basic properties.
Atoms are the building block of all matter. They have a positive nucleus, with positive protons, and neutral neutrons. In a large area surrounding the nucleus, is the electron cloud, made of negatively charged electrons.
An atom in its elemental state is always neutral.
When an element has a charge, it is because it has an unequal number of protons an electrons, making it an ion. Sometimes an element’s nucleus has an unequal number of neutrons and protons, making it an isotope. Carbon-14, for example, has 8 neutrons, instead of the 6 that Carbon-12 has. Carbon-14 is also a radioisotope, meaning it emits particles and decays at a rate called a half-life, making it useful for fossil dating. Along with that, radioactive carbon can be used as a tracer. This means it is incorporated in CO2 molecules and used to track metabolic pathways.
The location of the electron affects how the atom will react with other elements. When electrons are in the lowest available energy level, they are in the ground state. When they absorb energy, they move to a higher energy level, entering the excited state. For instance, when chlorophyll absorbs light energy, electrons within it are boosted to higher energy levels. This provides the energy necessary to produce sugar when they return to their ground state level as they release the energy they absorbed.
Bonding
Elements bond when two nuclei are attracted to each other. Energy is released when a bond is formed. All atoms want to either get rid of all their electrons on their outer shell or fill their outer shell with 8 (or in hydrogen’s case, 2) electrons, which makes them stable. There are 3 kinds of bonds, but for biochemistry, Ionic and covalent bonds are what is relevant.
Ionic bonds form ions (hence the name.) They occur when electrons are transferred. The atom that gains electrons becomes a negatively charged anion. The atom that loses electrons becomes a positively charged cation.
Covalent bonds are made when electrons are shared. This occurs when the two atoms have electronegativities that are closer together than in an ionic bond. Electronegativity is the tendency of an atom to pull electrons towards it. These bonds can be polar if the electronegativity is high enough. A polar molecule is a molecule with a partial charge. For example, water is a polar molecule, as oxygen is extremely electronegative, and water is partially electronegative.
Hydrogen Bonding
Hydrogen bonding is a specific kind of intermolecular force that is essential to life. It is what keeps the 2 strands of DNA bonded together, and gives water its unique characteristics. Since oxygen has a partial negative charge, and hydrogen has a partial positive charge, they are naturally drawn to each other.
Hydrophobic vs Hydrophilic
Polar molecules are hydrophilic. This is because they are attracted to the partially charged ends of water. Hydrophilic means they are attracted to water. (Not in that way… sick) NaCl or table salt is hydrophilic. This is why salt dissolves in water.
Non-polar molecules are hydrophobic. This means they are repelled by water. (They’re filthy water haters.) Lipids are hydrophobic, which is why fats and oils do not dissolve in water.
The cell membrane is a phospholipid bilayer, only allowing nonpolar substances to dissolve through it. Large polar molecules have to use specific hydrophilic channels.
Characteristics of Water
Water is a unique molecule, and without its unique properties, life on earth would not exist as it does, or even at all.
Water has a high specific heat: Because hydrogen bonds are so strong, it requires a lot of heat energy to break them. This is why large bodies of water remain the same temperature, and why coastal cities have a consistent temperature because the water absorbs all the heat energy before it can warm up.
Water has a high heat of vaporisation: A large amount of energy is needed for water to vaporise, which is why sweating is such an effective cooling method.
Water has high adhesion properties: Adhesion is when one substance clings to another. Adhesion causes capillary action, which occurs in the xylem of plants, and is used to bring water up from the roots without expending energy.
Water is a universal solvent: Due to its high polarity, water makes an excellent solvent.
Water is extremely cohesive: Molecules of water tend to stick to each other. This is observed in surface tension and allows for small insects to run across the surface of the water. Cohesion is also necessary to bring water up from the roots, by transpirational-pull cohesion tension.
Ice is less dense than water: Instead of freezing all the way through, ice crystallises, leaving large amounts of space, causing ice to float. This is essential for the survival of marine life during the winter, as they can live beneath the ice.
pH
pH is calculated by taking the -log of the chance of finding hydronium (H30+) ions within a certain amount of water. Hydronium is made in rare circumstances, where a hydrogen ion breaks off from a water molecule. Normally, there is a 1 in 10 million chance of there being a hydronium ion. This is the equivalent of 1x10^-7. The -log of this number is 7, the neutral pH.
Any pH below 7 is acidic. Any pH above 7 is basic. Stomach acid has a pH of 2, while bleach has a pH of 11. Human blood has a pH of around 7.4
Most living cells need to have an internal environment with a pH of around 7. Buffers exist to regulate pH by either absorbing excess hydrogen ions or donating missing hydrogen ions. In human blood, the bicarbonate ion (HCO3) is essential.
Macromolecules
There are 4 types of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates
Carbohydrates are made of carbon, hydrogen, and oxygen. They supply quick and easy energy. 1 gram of all carbohydrates will release 4 calories of energy. In our diet, they can be found almost everywhere in foods such as rice, pasta, bread, cookies, etc.
There are 3 kinds of carbohydrates: monosaccharides, disaccharides, and polysaccharides.
Monosaccharides
All monosaccharides have a chemical formula of C6H12O6. It is the placement of the carbon, oxygen, and hydrogen that determines its properties. Glucose, fructose, and galactose are all examples. They are isomers, meaning they have the same chemical formula, but a different structure.
Disaccharides
When 2 monosaccharides join together, they create disaccharides. They all have the chemical formula C12H22O11. Dehydration synthesis is the process that creates them. This process releases 1 molecule of water, hence the name. Lactose, maltose, and sucrose are all examples.
Hydrolysis is the exact opposite of dehydration synthesis. It is used during digestion. One molecule of water is used to breakdown polymers into monomers.
Polysaccharides Polysaccharides are long polymers of carbohydrates. Cellulose (plant cell wall), chitin (exoskeleton, fungi cell wall), glycogen (how animals store carbohydrates) and starch (how plants store carbohydrates) are all examples.
Lipids
Lipids include fats, oils, and waxes. Most contain 1 glycerol and 3 fatty acids. Glycerol is alcohol.
Fatty acids are the building blocks of lipids and are hydrocarbon chains with carboxyl groups at the end. There are 2 varieties; saturated and unsaturated. (3 if you count trans-fats when extra hydrogen is added to the fat to make the lipid solid)
Saturated fats are solid at room temperature, and are famously unhealthy as they are linked to heart disease.
Unsaturated fats are liquid at room temperature and are good dietary fats.
Lipids store much more energy than carbohydrates. 1 gram of any lipid will release 9 calories of heat per gram. They can be structural, as in the phospholipids of the cell membrane, or they can be hormones.
Proteins
Proteins are polymers of amino acids linked together by peptide bonds.
Amino acids are identifiable by their carboxyl group, amine group, and variable R, attached to a central carbon atom.
Proteins are complex and perform a vast array of duties, such as growth and repair, being enzymes, membrane channels, and hormones.
1 gram of protein releases 4 calories of heat.
Proteins contain the elements C H O N P S
There are only 20 amino acids coding for the thousands of proteins in the human body.
Protein Structure
There are 4 levels to the structure of a protein.
The primary structure results from the sequence of amino acids making up the polypeptide
The secondary structure results from hydrogen bonding within the molecule. This causes a helical structure
The tertiary structure is an intricate 3-dimensional shape or conformation of a protein and most directly decides the function of the protein. Enzymes denature in high temperatures or in the wrong pH because the tertiary structure is compromised.
The quaternary structure is only found in proteins that have more than 1 polypeptide chain, such as in haemoglobin.
Enzymes
Enzymes are large proteins
Enzymes lower the energy of activation, speeding up the reaction, as it lowers the amount of energy needed to start the reaction.
The chemical an enzyme works on is known as a substrate
Enzymes are specifically designed for specific substrates. For example, lactase only works on lactose. Notice the naming pattern for enzymes and their substrates.
The induced fit model is an explanation for how they work. When the substrate enters the active site, it induces the enzyme to change its shape to fit the substrate.
Enzymes can be reused as they do not degrade during a reaction
Enzymes are assisted by cofactors (minerals) or coenzymes (vitamins)
Prions
Prions are proteins that cause diseases. Mad cow disease is an example. It is a misformed protein able to influence other proteins to fold in the same way.
Nucleic Acids
There are 2 kinds of nucleic acids: RNA and DNA. They are necessary for carrying genetic information.
Nucleic acids are polymers of nucleotides
The nucleotides are the two purines: Adenine and Guanine, and the 3 pyrimidines, Thymine, Uracil, and Cytosine. Uracil is only found in RNA, and thymine is only found in DNA. Adenine connects with thymine/uracil, and guanine connects with cytosine.
i just learned from animal crossing that pondskaters stay on top of the water by secreting an oil from their feet
that seems kinda obvious in hindsight. i always figured they were just, like, light enough to not break surface tension
finally, some content! this was a quick info graphic I drew up on Procreate to revise for my ochem test tomorrow. disclaimer: I used information from this source (https://www.masterorganicchemistry.com/2010/05/24/imines-and-enamines/) since my own notes are based off lectures I received at my university that I’m not really allowed to share without heavy modification.
general post disclaimer: I’m an undergraduate student studying biochemistry and genetics. Posts are made for the purposes of education, revision and aesthetics. Not all the content I produce can be taken as entirely accurate and I do not take responsibility for errors made as a result of using this resource. Always consult course textbooks and lectures to aid in your specific learning outcomes. Do not repost without the original caption citing any extra references I used to make this post or remove my watermark. Other posts can be found on my blog as-studypeach@tumblr.com. Any problems, feel free to get in touch via my messages.
Chocolate is often considered an aphrodisiac and a mood booster because: It has feel-good chemicals – like PEA and serotonin – that can make people feel happy or loved.
To Any Biochemists or Any Aspiring Biochemists on Tumblr
So, I’m writing an Orginal character who is specializing in the Biochemistry field, and I want him to be as somewhat realistic as possible. I know that fictional characters don’t have to so accurate that they could be your next door neighbor, but I just want to know the broad strokes of your job and what you do because I’m extremely tired of people’s jobs being hyper fictionalized and inaccurate (Hackers, Scientists, Coders. Etc). So if you feel comfortable taking this survey, it would be greatly appreciated
1.What do you actually do?
2.What is one thing you like about your job?
3.What is one thing you dislike about your job?
4.How would you describe your personality? (I am aware this answer varies from person to person and it is nothing to be ashamed about)
5.Please describe the basic lab rules/protocols(If you have any)
6When is the appropriate time to wear lab coats?
7.What is one thing most media gets wrong about your job?
8.If you got a mysterious letter asking you to work at a strange company would you take it?
9.Do you like cats or dogs better?
10.What is your preferred weapon that you could find in a lab?
(Thanks for taking this survey and have a nice day:D)
✨Introductions✨
Pronouns: She/her
Studying: Forensic Science with an emphasis in chemistry and biochemistry
Country: 🇺🇸
Hobbies: reading, stardew valley, watching movies (I take 15-19 credit hours a semester while working a part time job at a restaurant and having and officer position in my sorority I don’t have much free time) I also have a fish!
Intro: Hi! I will be posting mostly how productive I was each day along with some book reviews and forensic science facts I like! Along with personal journeys with myself! (And occasionally fish updates :))
Did I skip my lecture to work on my lab report that I didn't do this weekend...? Yes. But at least I'm getting it done. Been feeling incredibly tired lately, however.
Today's goals:
● Finish Lab Report
● Take notes on lecture slides
● Sleep early
Sometimes you just have to lower your expectations a little and take care of yourself I guess.
🎼 : Blue World - Mac Miller
📖 : To Kill A Mockingbird - Harper Lee
Lol, my favorite thing is an alarm, I need to take my meds, so set an alarm for it. Study Time puts the alarm at the beginning and the end so I don't over just in case I have something else to do. P.S. Not everyone needs to do this but I like to label the alarms so that remember what to do when the time gets there.
adhd study affirmations + tips to stray from discouragement by a stem student with adhd.
you’re not always going to be consistent. you’re not always going to be motivated. you’re not always going to be efficient. and that is okay.
and the fact that you even got this far is an accomplishment in and of itself. In this line of work, people aren’t always the kindest to neurodivergent people especially since our symptoms can often hinder our performance academically.
if you’re good to go after reading the above, I’ve also made a post regarding adhd study tips that I haven’t seen anywhere else. But, if you’re burned out like me, feel free to keep reading.
honestly, these might serve a bit more as reminders because they’re kinda simple but even I needed this, so, here we go.
do not seek advice from anyone neurotypical unless it genuinely helps you. I cannot tell you the amount of time and tears I could have saved if I just considered the fact that just because popular self-improvement tips or study techniques didn’t work for me, it doesn’t mean I’m stupid or useless. It simply means our brains isn’t motivated by the same things neurotypical ones are, and therefore a lot of popular self-improvement videos or study tips aren’t going to work for you because 90% of the time, they’re not designed to work for neurodivergent people. So if you’d like to seek help in this area, look for tips and videos that ARE for neurodivergent people.
you might experience burnout a lot more than others. again, that is fine. if this doesn’t apply to you, great! Feel free to skip to the next tip/affirmation. If this does apply to you, read this carefully; if you’ve had any sort of streak in studying right now, chances are you know at least a portion of your studies were led purely on interest, curiosity or even novelty, as these are what keep us engaged in our studies. Knowing this, it is natural for you to experience burnout more frequently than others due to the possible hyperfixations that have been forming around your work. If you get burned out, please remember to take a break for a day and make sure it is efficient. Like your studies, your breaks are the key to having efficient study sessions in the future. So please treat yourself, especially if you’ve been working extra hard!
do not admire studious fictional characters unless it genuinely helps you or they too are neurodivergent. I know this technically could have been thrown in with tip number 1 but I felt like this tip alone is so important, because nowadays I see a lot of study tips with the title, ‘how to study like (insert studious fictional character here)’ and when I look at the post it kinda repeats the same few study tips I see all the time like ‘stay organized’ or ‘time block your day’ and I feel like admiring fictional characters who do things that don’t work for you can be damaging for your mental health, because we’re already told by neurotypical people all around us that we’re slow or lazy just because we don’t do things the way they do, and I think idolizing neurotypical people that make us feel bad at the end of the day just further promotes that kind of toxic thinking.
expect that a routine/schedule/technique that has been working for a while now may not continue to work in the future. things will always have to be new for us to be interested or engaged, that being said, if you expect this in the future you won’t be frustrated with yourself because you already had this in mind. It doesn’t mean you’re not smart. It doesn’t mean you’re lazy. It doesn’t mean you’re useless. It just means that you’ve done what you could, and now it’s time to move on to another routine/schedule/technique.
keep doing the things you love alongside work. I find that because our symptoms may cause us to fall behind on our studies, we tend to neglect our other needs as human beings just to make up for the fact that we simply do not learn or pick things up the same way neurotypical people do. Your hobbies and interests need to be part of your day, just as your studies do, even if you may take longer to learn things or remember important concepts in your studies. Neglecting your hobbies or interests can lead to even more frequent burn outs and even a relapse in depression and anxiety, so please take care of yourself and recognize that you need and deserve these things just as much as anyone else.
regularly discover what works for you on your own. here’s the thing; neurodivergent or not, no two brains work the same. Of course it is good to try out advice or tips you find online because they’re backed up by experience, but they’re backed up by that person’s experience with working with their own brain. So naturally, you need to find what works with your brain. Be open to trying everything, even the tips that are discouraged like listening to lyrical music while studying. That was the only way I learnt that this tip actually does help me at times, even when many people have said that it negatively affects your focus.
that’s all I have right now guys, I think I’m experiencing burn out or probably falling back into depression again so more than anything this also served as a reminder for me, but I really hope it also helped you guys nonetheless.
As always, tell me if you guys would like more posts like these and I’ll be happy to make more <33 please take care of yourself guys, and remember that your studies is just one aspect of your life. There are other aspects that need your care and attention too.
I resign my hatred for biochem for one day
when it takes you a while to process what someone is saying and you realize they asked you a question
