METABOLISM AND OTHER BIOCHEMICAL REACTIONS - BIOCHEMISTRY - The Handy Chemistry Answer Book (2014)

The Handy Chemistry Answer Book (2014)

BIOCHEMISTRY

METABOLISM AND OTHER BIOCHEMICAL REACTIONS

What is a fatty acid, and what is the difference between saturated and unsaturated fats?

Fatty acids are long, organic molecules that contain a carboxylic acid functional group at one end (see the picture below) and a long, nonpolar tail at the other end. They are an important source of energy in the body because they can be metabolized to generate ATP, which the body uses as fuel. When you’re looking at the nutrition information on your food, the concept of saturated versus unsaturated fats can be understood by looking at the structure of a fatty acid. Saturated fats are those that contain only single bonds connecting each carbon atom in the chain. Recall that double and triple bonds are called units of unsaturation. Unsaturated fats are any fats that do have units of unsaturation, or, in other words, that do have double bonds between some of the carbons in the chain. All fats are either saturated (top illustration) or unsaturated (bottom illustration).

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The structures of a sampling of vitamin molecules.

You might ask then, what is this “trans fat” everyone talks about in foods? First we should point out that most of the double bonds in unsaturated fats are in the cis conformation (where both carbon substituents are on the same side) in nature. Trans fats are fats that have had hydrogen artificially added, which can result in unsaturated fats with a trans conformation about the double bond. There is evidence that these trans fats can be more harmful to your health than other fats.

What is a lipid?

Lipids are a broad class of nonpolar or amphiphilic molecules including fatty acids, vitamins, sterols, and waxes, among others. An amphiphilic molecule is one that has both hydrophilic and hydrophobic groups, meaning that some parts of the molecule interact favorably with polar groups while other parts do not.

What do the chemical structures of vitamin molecules look like?

Above are the structures of some common vitamin molecules. They typically have a molecular weight in the neighborhood of 100–1500 g/mol.

What is a lipid bilayer?

Lipids are important in cells as they form bilayers that protect the cells and hold them together. In a lipid bilayer, the nonpolar tails gather on the inside of the bilayer, allowing the polar ends of each lipid molecule to interact favorably with the polar, aqueous environment of the cell and its surroundings. Within a bilayer, the lipid molecules can still slide around and can even flip from one side of the bilayer to the other. Lipid bilayers generally don’t allow molecules or ions to pass readily, allowing for the buildup of concentration gradients between the cell and its surroundings. Lipid bilayers are also found elsewhere; for example, they can also form separate compartments within cells.

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In a lipid bilayer (the layers in the middle that look like rows of clothespins), the nonpolar tails gather on the inside of the bilayer, allowing the polar ends of each lipid molecule to interact favorably with the polar, aqueous environment of the cell and its surroundings.

What is a biochemical pathway?

A biochemical pathway is a cycle of chemical processes that mutually interact to effect some purpose important for biological function.

What is a chemical-signaling molecule?

Chemical signaling molecules are small molecules that act to carry a message in a biological system. A cell can secrete signaling molecules and allow them to diffuse through the bloodstream. Signaling molecules can also be stuck to the surfaces of cells. It would be impossible to give a comprehensive description, so we’ll just mention a couple of examples of chemical signaling. Apoptosis, which is the intentional death of a cell, is a process that involves chemical signaling. An external signal reaches the cell, which sets off a series of reactions inside the cell, ultimately leading to its death. Calcium ions are another species often involved in cell signaling as their concentration affects the activity of many proteins and is also important for telling cells when to reproduce. Hormones are another type of chemical signals. They travel through our bodies, controlling growth of muscles and tissue, our reproductive systems, and our metabolism, among other things. These examples are just a small sample of the huge number of processes controlled by chemical signaling.

What is the Krebs cycle?

The Krebs cycle (also known as the citric acid cycle or the tricarboxylic acid cycle) is a biochemical process through which organisms can generate energy (in the form of ATP, or adenosine triphosphate) by oxidizing acetate that comes from other biomolecules (sugars, fats, and proteins). Since it uses oxygen, it is called an aerobic process. The Krebs cycle also generates other molecules, such as NADH (nicotinamide adenine dinucleotide), that are used in other biochemical processes. The names citric acid cycle and tricarboxylic acid cycle come from the fact that citric acid is used up and then regenerated in the reactions in the cycle. The name Krebs cycle is named after Hans Adolf Krebs, who was one of its discoverers.

What is binding affinity?

Binding affinity is used to characterize how strongly two molecules interact. Typically this will be a ligand and a receptor site, perhaps in a protein. Another common example would be a drug molecule binding to a receptor site somewhere in the brain. In simple cases where one drug molecule (D) binds to one receptor molecule (R) to form a complex (DR), the binding affinity can be described by the equilibrium constant:

Keq = [DR]/([D][R])

The binding affinity can be looked at as a measure of how strongly a molecule binds to its receptor site. If a drug has higher affinity for its binding site, less of the drug will be required to achieve a response. Typically scientists designing pharmaceuticals would like a drug to have a high binding affinity for its receptor so that it can effect a strong response.

How is O2 transported through the body?

Oxygen enters our body through our lungs in the air we breathe. O2 makes up about 21% of the total volume of air on Earth. From the lungs, O2 diffuses into the bloodstream, where it binds to a molecule called hemoglobin in our red blood cells. The binding affinity of O2 to hemoglobin is pH-dependent such that oxygen can readily be picked up by red blood cells near the lungs and then released into tissues and other areas of the body that need it.

What is cooperativity?

Cooperativity describes how the binding affinity at one site of a protein affects the binding affinity at another site. In hemoglobin, for example, there are four sites at which oxygen molecules can bind. After the first oxygen molecule binds, conformational changes take place in the rest of the protein that increase the binding affinity at the other sites. The second oxygen is then able to bind even more easily, and the third and fourth even more easily yet. This gives rise to a sigmoidal-curved shape in a plot of the fraction of hemoglobin bound by O2 versus the partial pressure of O2 (see illustration).

Similar binding curves result in other examples of cooperativity, though the example of hemoglobin is probably the most commonly discussed example of the phenomenon.

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A graph describing cooperativity in hemoglobin.

What is ATP?

ATP, or adenosine triphosphate, is a molecule used as a source of energy in the body. The energy of an ATP molecule is stored in its chemical bonds, and it is released through hydrolysis of phosphate groups to form ADP (adenosine diphosphate). The ATP in our bodies is continuously recycled, and on average, each ATP molecule in our body will be used and regenerated over one thousand times each day.

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How does blood clotting take place?

Platelets in the blood send a message to constrict blood vessels in the area surrounding a wound. Platelets gather to block the flow of blood coming out. At the same time, a chemical messenger called prothrombin activates an enzyme called thrombin, which then produces a species called fibrin. Fibrin forms threads to block the wound even better.

What is a kinase?

Kinases are a class of enzyme that is responsible for transferring phosphate groups (see image below) from donor molecules, such as ATP, to substrates during a reaction called phosphorylation. These are typically named for their substrate: for example, a tyrosine kinase catalyzes the transfer of a phosphate group to a tyrosine residue of a protein. Kinases are part of a larger group of enzymes called phosphotransferases, all of which carry out chemistry involving phosphate groups, shown below.

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How do your muscles work?

Muscles allow you to exercise and move heavy objects and are necessary for basic activities like breathing, pumping blood, and pretty much anything else you do. On a molecular level, muscles work based on the binding, movement, and rebinding of molecules called actin and myosin. This process involves the hydrolysis of ATP to generate energy.

For your muscles to move, myosin first attaches to actin, forming a bridge. At this point, ADP and a phosphate group are attached to the myosin. The myosin bends (this is what actually controls movement), releasing the ADP and phosphate. Then a new ATP molecule binds again, and then the myosin releases the actin. The ATP is then hydrolyzed, putting the myosin back into its original position, at which point the cycle can begin again.

What is rigor mortis?

Rigor mortis is the stiffening of the muscles that occurs shortly after death. Since very little or no ATP is present, muscles are left contracted, stiff, and unable to relax.

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The molecules actin and myosin bind, move, and rebind within your muscle fibers in order to provide movement.

What determines whether a cell is a skin cell, blood cell, etc.?

The process that new cells undergo to become a specific type of cell is called cellular differentiation. Interestingly, different types of cells don’t contain different genetic information, but rather they just express different parts of their genetic information. Signal molecules tell the cell which parts of its DNA to express, which in turn controls what types of proteins and other molecules are present in the cell, and ultimately these factors determine its function.

How does photosynthesis work?

Photosynthesis is the process carried out by plants to harvest energy from sunlight. The most important molecule in photosynthesis is called chlorophyll; it’s what collects sunlight and gives plants their green color. Carbon dioxide (CO2) is taken in through cells called stomata, and the plants also draw water up through the roots and into the leaves. The reaction catalyzes when chlorophyll absorbs light and makes ATP along with another molecular energy source called NADPH (nicotine adenine dinucleotide phosphate). In the process, CO2 is used up and water molecules are split, releasing O2 gas, which other organisms (like humans and animals) can then breathe.

How do living things store fat?

Fat is stored in a type of tissue called adipose tissue. This is made up of cells called adipocytes that store lipid molecules to be used for longer-term energy storage.

What causes addiction to a substance?

Drugs that cause addiction change the ability of receptors in your brain to cause you to feel pleasure. There are a few ways this can happen. Depressants often work by increasing the affinity of a receptor for a small molecule called GABA (gamma-aminobutryic acid). Stimulants make you feel happy or better than you would otherwise. They can do this in a few different ways, but two common ones are to either cause more dopamine to be released or to prevent the reabsorption of dopamine so that it stays around and keeps you happy for longer. Narcotics act in a similar manner to stimulants in that they mimic the molecules that make you happy normally.

What gives some people such a high alcohol tolerance?

From the biochemical point of view, the amount of the enzyme alcohol dehydrogenase in a person’s body determines how rapidly their body can process alcohol. People with more alcohol dehydrogenase can convert ethanol (which is what gets you drunk) to acetaldehyde faster. A person’s body size also is important, though. Bigger people have more mass to spread the alcohol around so their blood concentration of ethanol doesn’t rise as fast as that of smaller people.