Biochemistry

Introduction

Dear science-enthusiast,

We welcome you to our lecture about biochemistry - a science on the border of biology and chemistry. It studies a vast variety of molecules and reactions presented in living organisms.  We will focus on the main classes of biomolecules, such as carbohydrates, proteins, lipids, nucleic acids (you may know them as DNA and RNA) as well as their interactions. In this lecture we will explain what makes their structure and functions so special. Experiments provided by biobranches.com for the following lecture will cover the main characteristics of biomolecules as well as different biochemical reactions.

What does biochemistry study?

 

The main atom in all biomolecules is carbon. We can even say that everything consists of carbon and other atoms are just small additives. Carbon became so ‘successful’ due to its unique ability to create bonds with up to four atoms (carbon or otherwise). This allows for the emergence of long strings or circles of carbons. Carbon can be called a ‘friendly’ element because unlike some other atoms it does not have the desire to steal any electrones when joining electron clouds in order to form bonds. This approach allows carbon to maintain respectful and stable relationships with its partners. Also it is a relatively small atom which perfectly fits into complicated molecules without causing additional internal spatial tension. The second most common element is hydrogen which usually attaches to a carbon-atom in case it has free bonds .Other atoms, like nitrogen, oxygen, phosphorus, sulfur can also form bonds with carbon, and together with hydrogen, they make up more than 99% of biomolecules and therefore a cell mass. Those additives usually form and serve as various functional groups changing and regulating functions of the complex biomolecules.

 

Such complex biomolecules are often polymers composed of many repeating simple and similar molecular subunits. These macromolecules are extremely big and heavy and therefore their synthesis is a major energy-consuming activity of cells. Macromolecules are easily categorized into several types according to the structure of subunits.

Probably, the most famous macromolecules are the nucleic acids - polymers of specific subunits, called nucleotides. Nucleic acids store and transmit genetic information which is coded by the sequence of different nucleotides. There are two main types of nucleic acids - one is DNA (deoxyribonucleic acid), formed by two polynucleotide chains wrapped into a double stranded helix. This nucleic acid plays a role of a safe deposit for information and since information is very valuable for the cell, DNA is almost exclusively found in the cell nucleus. Another nucleic acid is RNA (ribonucleic acid), which is also assembled as a chain of nucleotides, but unlike DNA, RNA is a single strand folded onto itself, rather than a paired double helix. RNA is assembled as a copy of the sequence of DNA in the nucleus and in the majority of cases serves as a unidirectional vector transmitting information from the nucleus to the cytoplasm. Through this approach, the cell is able to isolate storage of the information from its utilization and improve the level of DNA stability and integrity.

In the cytoplasm RNA molecules become a template for the protein synthesis. Proteins also exhibit a polymeric structure and their subunits are represented by amino acids. Variable sets of three nucleotides in the RNA specifically code for one amino acid in the protein, thus forming a particular protein (take a ). This is usually referred to as central dogma of molecular biology and explains the flow of genetic information: "DNA makes RNA, and RNA makes protein".

Proteins constitute the largest fraction (besides water) of a cell. They are both main executors in all cellular processes and structural blocks building of the cell. Proteins that are able to catalyze and speed up chemical reactions are called enzymes. Without enzymatic activity no organism would be able to live because all viable reactions would happen too slow. Proteins also play an irreplaceable role in cell signalling when embedded in cell membranes or floating in the cytoplasm. Others serve as molecular machines with moving parts helping to transport different molecules. Antibodies, hormones, elastic fibers, sources of luminescence are all proteins. Catalogues of their many functions are countless and can be found on https://www.rcsb.org/.

There are two other crucial types of polymeric macromolecules in the cell - carbohydrates and lipids. Both of these molecules are generated in the living cell by subsequent actions of protein enzymes, which once again shows why proteins are the main actors in biochemistry.

Let's start with carbohydrates. Subunits in these macromolecules are simple sugars among which glucose or fructose, these are often called polysaccharides. Polysaccharides have three major functions in the cell. Firstly, they serve as energy-rich fuel storages, for example glycogen in the human liver or starch in potatoes. Secondly, they play a role in the formation of rigid cell walls in plants (cellulose), bacteria (murein) or fungi (chitin). Thirdly, shorter polymers of sugars (oligosaccharides) attached to proteins or lipids on the cell surface serve as specific cellular signals.

The lipids are usually very easy to distinguish with the naked eye because they don't mix with water. This effect can be observed for instance when lipid-rich butter or olive oil is added to water. Unlike previously mentioned macromolecules, polimeric lipids contain not only uniform subunits but rather a combination of two molecules - a ‘head’ (glycerol, phosphate etc..), and one or several ‘tails’ - long hydrocarbon chains (also known as fatty acids). Such hydrocarbon chains are extremely energy rich which makes lipids a perfect energy depository. However, lipids play an even more fundamental role as the main structural components of cell membranes. As we will see in paragraph 3.3 the formation of cell membranes by a specific type of lipid - phospholipids corresponds to their dual nature where one part is hydrophobic and therefore avoids the contact with water, and the other part is hydrophilic i. e. attracted to water.

3.1 Enzymes and carbohydrates

When an animal is hungry it starts to look for energy rich food sources, and it finds this, for example, in food with a high polysaccharides content. However, digestion of polysaccharides is not very easy and requires assistance of special protein enzymes. Because enzymes break down bonds inside polysaccharides between simple sugars, these sugars are later preconditioned to release energy during the following digestion phases. Animals have gained various enzymes able to digest different polysaccharides. For example, humans have enzymes called chitinases, which can break down bonds in one of the main components of fungi- chitin. However, we are not able to digest cellulose ourselves and only bacteria which live in our intestines can help us with that.

Enzymes start to interact with food right after it enters our mouth and one of the first enzymes in action is salivary amylase. This enzyme splits starch - a polysaccharide consisting of numerous sugar units found in sweet and common potatoes, rice, beans and etc.  Later, the process of starch digestion is completed in the small intestine by another enzyme called pancreatic amylase.

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Many mammals have seen great expansions in the number of copies of the amylase gene possibly caused by increased starch consumption by these species. This allowed them to boost expression of amylase and therefore digest starch faster and more efficiently.  

Another interesting example of polysaccharide digestion is the ability of some adults to digest lactose - milk sugar. In general, mammals can consume milk only in childhood and after reaching a particular age the enzyme, lactase, required for the digestion of lactose is absent in these species. However, 35 percent of the global human population — mostly people with European ancestry — can digest lactose in adulthood without a hitch. These people inherited a mutation in the gene that repressed the shutdown of the lactase gene. Such an evolutionary advantage allowed our ancestors to consume highly nutritious cow milk which they obtained from their cattle and to inhabit some territories with harsh climates, like Scandinavia. Moreover, other studies found that some people from the Middle East and Africa also inherited mutations which made them ‘lactase persistent’ but these mutations happened independently from the european one. This is a very recent example of natural selection in humans, people that were able to digest milk, were more and left more suited for survival and therefore were able to have more offspring. That is how changes in the DNA, proteins and other macromolecules are interconnected.

If you want to know how to determine the presence of starch in common food we welcome you to subscribe to our youtube channel and take a look at the first biochemistry lesson.

3.2 Proteins and peptide bonds

As we mentioned, proteins are main acting units in the cell and specific sequences of monomeric subunits inside them, presented by amino acids which are linked in characteristic linear structures, give rise to various discrete functions. One particular polymeric sequence of amino acids produces the most abundant protein in mammals, an extracellular component of connective tissues - collagen; another produces a protein that transports oxygen in the blood - hemoglobin; a third speeds up a reaction necessary for digestion of starch (amylase) and so on.

Notably, the proteins of every organism, from bacteria to humans, are constructed from the same set of 20 amino acids. Combinations of only 20 amino acids linked in different order are resulting in strikingly diverse characteristics of proteins. Moreover, human organisms, for example, are not able to produce 8 of these 20 amino acids and we can get them only from external food sources.The amino acids are connected by a so-called peptide bond - a specific bond for a protein. The formation of such bonds consumes energy which is also gained by organisms from food.

Moreover, not only the linear amino acid chain in the proteins is responsible for their functions.

Every protein has a unique three-dimensional structure, which is maintained by non peptide bonds. Furthermore, big and complex proteins usually consist of more than one linear amino acid chain, which are called domains and each domain performs one discrete function in these complex proteins. Such molecular machineries combine simple roles of the domains and are able to perform incredible things, such as rotating and transforming the energy of the proton flow into stored energy (this protein is called ATP synthetase). They do this  in the same manner as wind and hydro power plants.When such a structure is disrupted it leads to total alteration of the protein and abolishment of its activity. This process is called denaturation and can be caused by application of some chemicals, heat or radiation.

If you want to know how to determine the presence of proteins and therefore peptide bonds in common food we welcome you to subscribe to our youtube channel and take a look at the second biochemistry lesson.

3.3 Lipids and saponification

Our everyday routine always includes washing our hands, hair and bodies with soap. However, how this substance actually removes the dirt is not so obvious. After the premier of the movie Fight Club in 1999 relationships between soap production and fat (lipids)  became more famous. This reaction was discovered firstly in the beginning of the 19th century by French chemist Michel Eugène Chevreul and his early work with animal fats, which revolutionized the manufacturing of soap and candles. In 1811 he discovered that both animal and plant lipids react with alkali (NaOH or KOH) in the presence of alcohol when it’s heated. This reaction results in disruption of the glycerol ‘head’ of the lipid from the ‘tails’ which are presented by fatty acids. These fatty acid tails react with alkali (NaOH or KOH) and become fatty acid salts of Na or K and these salts are known as soaps. The main useful feature of the molecular structure of soap is its dual nature. Half of it stays insoluble in water (hydrophobic) and the other half is soluble and is called hydrophilic. This is what makes soap such a good cleaning agent. This dual nature results in the formation of the micelles, where hydrophobic parts with attached dirt particles are in the middle, and the hydrophilic ends create the surface of the soap droplet.

However, formation of micelles is important not only for everyday hygiene and prevention of diseases but also for cells - the smallest unit of all known organisms, from bacteria to the blue whale. Cells are separated from the external environment with a specific structure called membrane and the organisation of the membrane resembles the above mentioned soap micelles. A membrane also consists of dual nature molecules called phospholipids, where the phosphate head is hydrophilic and the hydrocarbon tails are hydrophobic. Thus, the biochemical structure of phospholipids is similar to the salts of fatty acids presented in the soap. However, in contrast to soap micelles, phospholipids can automatically form not only single-layered phospholipid micelles but also bi-layered structures in water, such as liposomes and cell membranes. The ability of phospholipids to self-organize in bilayers, probably played an important role in the formation of the first cells at the origin of life.

If you want to see how lipids can be turned into soap we welcome you to take a look at the third biochemistry lesson on our YouTube channel.