Biochemistry

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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.

Alkanes: Saturated Hydrocarbons

So you want to be an organic chemist? Well, learning about hydrocarbons such as alkanes is a good place to start…

Alkanes are a homologous series of hydrocarbons, meaning that each of the series differs by -CH2 and that the compounds contain carbon and hydrogen atoms only. Carbon atoms in alkanes have four bonds which is the maximum a carbon atom can have - this is why the molecule is described to be saturated. Saturated hydrocarbons have only single bonds between the carbon atoms.

The general formula of an alkane is CnH2n+2 where n is the number of carbons. For example, if n = 3, the hydrocarbon formula would be C3H8 or propane. Naming alkanes comes from the number of carbons in the chain structure.

Here are the first three alkanes. Each one differs by -CH2.

Shorter chain alkanes are gases at room temperature, medium ones are liquids and the longer chain alkanes are waxy solids.

Alkanes have these physical properties:

1. They are non-polar due to the tiny difference in electronegativity between the carbon and hydrogen atoms.

2. Only Van der Waals intermolecular forces exist between alkane molecules. The strength of these increase as relative molecular mass increases therefore so does the melting/boiling point.

3. Branched chain alkanes have lower melting and boiling points than straight chain isomers with the same number of carbons. Since atoms are further apart due to a smaller surface area in contact with each other, the strength of the VDWs is decreased.

4. Alkanes are insoluble in water but can dissolve in non-polar liquids like hexane and cyclopentane. Mixtures are separated by fractional distillation or a separating funnel.

The fractional distillation of crude oil, cracking and the combustion equations of the alkanes will be in the next post.

SUMMARY

Alkanes are a homologous series of hydrocarbons. Carbon atoms in alkanes have four bonds which is the maximum a carbon atom can have - this is why the molecule is described to be saturated. Saturated hydrocarbons have only single bonds between the carbon atoms.

The general formula of an alkane is CnH2n+2 where n is the number of carbons.

Shorter chain alkanes are gases at room temperature, medium ones are liquids and the longer chain alkanes are waxy solids.

They are non-polar.

Only Van der Waals intermolecular forces exist between alkane molecules. The strength of these increase as relative molecular mass increases therefore so does the melting/boiling point.

Branched chain alkanes have lower melting and boiling points than straight chain isomers with the same number of carbons.

Alkanes are insoluble in water but can dissolve in non-polar liquids like hexane. Mixtures are separated by fractional distillation or a separating funnel.

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amateurchemstudent

4 years ago

Around a year ago, scientists determined the structure of the SARS-CoV-2 spike protein. Here’s a look at how it was done and how it helped the fight against #COVID19 in the latest edition of #ChemVsCOVID with the Royal Society of Chemistry: https://ift.tt/3pZiZe9 https://ift.tt/3002NPh

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amateurchemstudent

4 years ago

Covalent Bonds: Sharing Is Caring!

Welcome to my second out of three posts on bonding - ionic, covalent and metallic. This post also covers the coordinate/ dative bond which I can’t remember if I’ve covered before. Only one more of this series left! Find the others here.

Covalent bonding involves one or more shared pairs of electrons between two atoms. These can be found in simple molecular elements and compounds like CO2 , macromolecular structures like diamond and molecular ions such as ammonium. Covalent bonds mostly occur between non-metals but sometimes metals can form covalent bonds.

Single covalent bonds share just one pair of electrons. Double covalent bonds share two. Triple covalent bonds share three.

Each atom usually provides one electron – unpaired in the orbital – in the bond. The number of unpaired electrons in an atom usually shows how many bonds it can make but sometimes atoms promote electrons to fit in more. Covalent bonds are represented with lines between the atoms – double and triple bonds represented with two and three lines respectively.

Dot and cross diagrams show the arrangement of electrons in covalent bonds. They use dots and crosses to demonstrate that the electrons come from different places and often only the outer shell is shown.

The simple explanation as to how atoms form covalent bonds is that one unpaired electron in the orbital of one atom overlaps with one in another atom. Sometimes atoms promote electrons in the same energy level to form more covalent bonds. For example, if an atom wants to make three covalent bonds but has a full 3s2 shell and a 3p1 shell, it can promote one of its 3s2 electrons so that an electron from the other atoms can fill the 3s shell and pair with the new 3p2 shell.

Sometimes promotion does not occur and that means different compounds can be made such as PCl3 or PCl5.

A lone pair of electrons is a pair of electrons from the same energy sub-level uninvolved in bonding. Sometimes these can form something called a coordinate bond, which contains a shared pair of electrons where both come from one atom. The lone pair of electrons is “donated” into the empty orbital of another atom to form a coordinate bond.

This is an example of a coordinate (sometimes called dative) bond between ammonia and a H+ ion which has an empty orbital. The lone pair on the ammonia overlaps with this H+ ion and donates its electrons. Both electrons come from the ammonia’s lone pair so it is a coordinate bond. This is demonstrated with an arrow. The diagram is missing an overall charge of + on the ammonium ion it produces. Coordinate bonds act the same as covalent bonds.

Once you have your covalent bonds, you need to know about covalent substances and their properties. There are two types of covalent substance: simple covalent (molecular) and macromolecular (giant covalent).

Molecular simply means that the formula for the compound or element describes exactly how many atoms are in one molecule, e.g. H2O. Molecular covalent crystalline substances usually exist as single molecules such as iodine or oxygen. They are usually gases or liquids at room temperature but can be low melting point solids.

Solid molecular covalent solids are crystalline so can be called molecular covalent crystals. Iodine and ice are examples of these. Iodine (shown below) has a regular arrangement which makes it a crystalline substance and water, as ice, has a crystalline structure as well.

The properties of these crystals are that they have low melting points, are very brittle due to the lack of strong bonds holding them together and also do not conduct electricity since no ions are present.

The other kind of covalent substance you need to know is macromolecular. This includes giant covalent structures such as diamond or graphite, which are allotropes of carbon. Non-metallic elements and compounds usually form these crystalline structures with a regular arrangement of atoms.

Allotropes are different forms of the same element in the same physical state.

Diamond is the hardest naturally occurring substance on earth therefore is good for cutting glass and drilling and mining. It has a high melting point due to the many covalent bonds which require a lot of energy to break. Each carbon has four of these bonds joining it to four others in a tetrahedral arrangement with a bond angle of 109.5 degrees and it does not conduct electricity or heat because there are no ions free to move.

Graphite, on the other hand, can conduct electricity. This is because it has delocalised electrons between the layers which move and carry charge. Carbon atoms within the structure are only bonded to three others in a hexagonal arrangement with a bond angle of 120 degrees. Since only three of carbon’s unpaired electrons are used in bonding, the fourth becomes delocalised and moves between the layers of graphite causing weak attractions, explaining why it can conduct electricity.

Graphite’s layered structure and the weak forces of attractions between it make it a good lubricant and ideal for pencil lead because the layers can slide over each other. The attractions can be broken easily but the covalent bonds within the layers give graphite a high melting point due to the amount of energy needed to break them.

SUMMARY

Covalent bonding involves one or more shared pairs of electrons between two atoms. Covalent bonds mostly occur between non-metals but sometimes metals can form covalent bonds.

Single covalent bonds share just one pair of electrons. Double covalent bonds share two. Triple covalent bonds share three.

Dot and cross diagrams use dots and crosses to demonstrate that the electrons come from different places and often only the outer shell is shown.

Sometimes promotion does not occur and that means different compounds can be made such as PCl3 or PCl5.

The formation of ammonium is an example of this.

There are two types of covalent substance: simple covalent (molecular) and macromolecular (giant covalent).

Solid molecular covalent solids are crystalline so can be called molecular covalent crystals. Iodine and ice are examples of these.

Giant covalent structures such as diamond or graphite are allotropes of carbon. Allotropes are different forms of the same element in the same physical state.

Diamond has a high melting point due to the many covalent bonds which require a lot of energy to break. Each carbon has four of these bonds joining it to four others in a tetrahedral arrangement with a bond angle of 109.5 degrees and it does not conduct electricity or heat because there are no ions free to move.

Graphite can conduct electricity. This is because it has delocalised electrons between the layers which move and carry charge. Carbon atoms within the structure are only bonded to three others in a hexagonal arrangement with a bond angle of 120 degrees. Since only three of carbon’s unpaired electrons are used in bonding, the fourth becomes delocalised and moves between the layers of graphite causing weak attractions, explaining why it can conduct electricity.

Happy studying!