Chemistry & Biochemistry I Flashcards
What is the definition of „Chemistry”?
the science that deals with the composition and properties of substances and various
elementary forms of matter (gas, liquid, solid).
What is the definition of “Biochemistry”?
the science concerned with the chemical and physicochemical processes & substances that occur within living organisms.
What is “matter”?
everything around us that has mass and occupies space.
– Atoms are small particles that make up matter - the “Lego bricks” that make up everything in our universe.
– Atoms are made up of electrons, protons & neutrons.
Chemical Elements:
• An element is a substance made up of just one type of atom so it cannot be split up into simpler substances.
• As with Lego, there is a finite number of different types of atoms from which we can build things.
• The elements we know of are in the Periodic Table.
• In Chemistry each element is given a chemical symbol for its long name. For example:
- Hydrogen – H
- Carbon – C
- Calcium – Ca
- Magnesium – Mg
Elements in the Human Body:
- 26 different elements are normally present in the human body.
- 4 major elements - carbon, hydrogen, oxygen and nitrogen, which account for 96% of the human body.
Elements in the Human Body:
- 26 different elements are normally present in the human body.
- 4 major elements - carbon, hydrogen, oxygen and nitrogen, which account for 96% of the human body.
Subatomic Particles:
Every element is made up of atoms. Each atom is made up of subatomic particles called protons, neutrons and electrons.
Protons and neutrons together form the nucleus of an atom.
• Protons have a positive charge and a mass of approximately 1 atomic unit.
• Neutrons have no charge and a mass of approximately 1 atomic unit.
• Electrons are negatively charged particles that ‘buzz’ around the outside of the nucleus,
creating an electron cloud. They have virtually no mass at all.
Electrons:
- An element will have an equal number of electrons and protons giving an overall neutral charge to the atom. Recall that electrons carry a negative charge.
- Electrons move in groups around the nucleus, known as ‘electron shells’.
- Within their shells electrons ‘pair-up’.
- An atom becomes reactive if its outer shell isn’t full or if it loses an electron.
- This happens in ‘free radicals’, where an electron become unpaired
Atoms Analogy:
“Atoms are like families”:
• Each proton is an adult with one child (an electron).
• Each neutron is an adult with no children.
• The adults hang out together in the centre (nucleus) - each weigh 1.
• The children (electrons) buzz around the adults like an excited cloud and weigh (virtually) nothing.
• Each parent (proton) has a positive charge and each child (electron) has a negative charge.
• The opposite charges attract each other, keeping the family together!
• All the chemical properties of an atom are down to its number of protons and electrons. The neutrons just add weight to the atom; they don’t significantly change how it chemically reacts.
The Periodic Table:
a list of all of the currently known elements, arranged in columns and rows that show us which elements share similar reactivity and physical properties.
- The number that is assigned to each element tells us how many protons and, therefore, how many electrons each atom has.
- The larger number is always the mass number (the weight in atomic units). It tells us how much the atom weighs so it can be used to work out the number of neutrons (remembering that electrons weigh nothing).
Halogens ➡️ iodine in thyroid health:
- If present in the body, the other halogens (e.g. fluoride & chloride) can enter the thyroid, preventing the formation of T3 & T4 (inducing hypothyroidism).
- Fluoride is in toothpaste, tap water and mouthwashes, whilst chlorine is in swimming.
Counting Subatomic Particles:
Atomic number = number of protons.
Mass number = number of protons + number of neutrons.
Number of neutrons = Mass number (always bigger) – atomic number.
Isotopes:
Isotopes = atoms of the same element which have a different numbers of neutrons in the nucleus (this does not affect the chemical activity of the atom as neutrons have no charge, but it does change the mass)❗️
• Some (but not all) isotopes have such an imbalance of protons (parents) and neutrons in their nucleus that it causes the atom (family) to become unstable.
• This is the cause of radioactivity. The unstable atom needs to get rid of energy to become stable.
*A ‘PET scan’ is an imaging technique used in allopathic medicine. Radioactive isotopes are introduced (often injected) into the body.
Isotopes in Medicine:
• Some diagnostic techniques in medicine use radioactive tracers which emit gamma rays from within the body.
• Radiotherapy uses the gamma rays from radioactive isotopes to target rapidly dividing cells. However, this is also highly damaging to healthy tissues.
• The breath test for H. pylori uses urea labelled with either radioactive carbon-14
or non-radioactive carbon-13. In the subsequent 10–30 minutes, the detection of isotope-labelled carbon dioxide in exhaled breath indicates that the urea was split; this indicates that urease (the enzyme that H. pylori uses to metabolise urea) is present in the stomach, and hence that H. pylori bacteria are present.
Electron Shells:
- Electrons like to “hang out” in certain numbers (2, 8, 8, 8)
- Electrons always want to be in pairs.
- All of the reactions that happen in Chemistry are driven by atoms trying to end up with a stable and full outer shell either by stealing, giving away (donating) or sharing electrons.
Hydrogen - The Simplest Atom of All:
- Hydrogen contains: One proton, One electron. No neutrons.
- We often refer to Hydrogen, when it is in its H+ form (hydrogen minus the electron’), as being a ‘proton’. This is why we talk about acidity in terms of protons.
- Because hydrogen has only one electron in its outer shell, it will often go looking for another atom that needs one electron to fill its shell. This means that hydrogen easily reacts with other atoms.
- Some elements do not easily react as they have their outer shell filled with the perfect number, so they are rarely involved in chemical reactions. We call these elements ‘inert’.
Bonding:
- Atoms that are trying to become stable by bonding with other atoms so that they can get just the right number of electrons in their outer shell.
- The two main types of bonding are:
- Ionic bonding – atoms transfer electrons (1 donates, 1 receives).
- Covalent bonding – occurs when atoms share electrons.
Ionic Bonding:
- Ionic bonds occur when one atom donates some of its electrons to another.
- This usually only occurs when there are 1, 2 or occasionally three electrons to donate.
- Moving any more electrons than this isn’t energetically favourable.
- Consider the regular appearance of table salt (NaCl) and Sea/Himalayan salt (which contain various other minerals, too).
Ions:
- If an atom gives up or gains electrons to fill its outer shell, it becomes an ion.
- Ionisation is the process of giving or gaining electrons.
- Ions are written with their corresponding – or + charge.
For example:
• Ca2+ has donated two electrons to another element and now has a positive charge.
• Cl ̄ has gained an electron so has taken on a negative charge.
• In both cases the Calcium and Chlorine have ended up with a full outer shell.
Sodium Ion:
- Sodium has one electron in its outer shell.
- Energetically its far easier to give that one electron away than to gain or share 7.
- So sodium always gives its one electron away to become Na+.
Covalent Bonds:
- occur when two elements share electrons (so that they both have the “magic number” they are looking for).
- This kind of bonding tends to happen when the two atoms are similar or when there are a lot of spaces to be filled to reach a full outer shell.
Polar Bonds:
•form where electrons are shared unequally.
This happens because some atoms have a lot of ‘electron pulling power’: F, Cl, O and N are the most electronegative elements
Some elements have lots of protons compared to the number of electron shells i.e. a strong positive centre. These elements are referred to as ‘electronegative’ because they tend to pull the shared electrons towards themselves.
•These very electronegative atoms are able to pull the electrons in a bond towards them, leading to an uneven distribution of charge.
Hydrogen Bonding:
• One of the most important examples of a polar bond are the bonds between Oxygen and Hydrogen in water‼️
• The oxygen pulls the electrons towards itself, resulting in a negatively charged area over the oxygen and a positively charged area over each hydrogen.
• The positive hydrogens on one water molecule are attracted to the negatively charged oxygens on the next molecule.
• These loving interactions are called hydrogen bonds and are what give water many of its
special properties such as surface tension and the ability to dissolve so many different things.
Water - The Universal Solvent:
- Water serves as the medium for most chemical reactions in the body.
- As water contains polar bonds, it is an ideal solvent for dissolving chemicals into their separate ions. In addition, the different electrical charges in water can allow water molecules to become attracted to other molecules (hence water dissolves salt).
- Hydrophilic molecules are molecules which have polar bonds. They dissolve easily in water (e.g. alcohol).
- Hydrophobic molecules contain non-polar covalent bonds, so they do not dissociate easily in water (e.g. fats).
Electrolytes:
• An electrolyte is formed when an ionic compound (e.g. salt) dissolves in water.
• Electrolytes can conduct electricity.
• The key electrolytes in the body include Sodium, Potassium, Chloride, Calcium, Magnesium, Phosphate, Bicarbonate.
• Electrolytes are important body constituents because:
- Conduction of electricity is essential for nerve & muscle function. - They exert osmotic pressure important for water balance.
- Some play an important role in acid-base balance.
Acids and Bases:
- An acid is a substance that releases a high amount of H ions when dissolved in water.
- A base is a substance which binds to hydrogen ions in solution. This creates lots of OH-.
- Water is a neutral solution because for every H+ released an OH- is also created. Although, if you steal H+ from a water molecule (H2O), you are left with lots of OH-
- The pH scale was developed using water as a standard. The pH of water is 7. Anything with a pH lower than 7 is an acid and anything higher than 7 is considered a base (alkali).
• The blood closely monitors and maintains an optimal pH of 7.35-7.45 for chemical reactions to occur, whilst the stomach has an optimal pH of 2-3.
Acids and bases in food:
- Fruit and vegetables contain organic acids and hence may have a low pH when measured as foods before consumption. Yet these organic acids can be metabolised by the body and intestinal bacteria to become alkaline. These foods are also high in alkaline minerals, e.g. potassium, magnesium and calcium which contribute to their net alkaline effect.
- dairy, meat very acidic due to high protein/sulphur amino acid content.
- Other acidic foods are those rich in refined sugars and processed foods, stress and being sedentary also create an acidic environment.
Testing pH in the Body:
• Using a strip of pH (litmus) paper:
- Urine: Urinate onto a strip on your second urine output in the morning (about an hour
after your first urine output upon waking). Measure the pH midstream.
- Saliva: Wash your mouth upon waking with plain water. Wait for about ten minutes and then spit onto the pH paper.
Chemical Reactions:
- Chemical reactions occur when new bonds are formed or old bonds are broken between different molecules.
- Every reaction involves the transfer of energy to either potential (stored) energy, kinetic energy or heat.
- The starting materials are known as the reactants and the end molecules are known as the products.
- Reactions are written in formula and they must always balance in electrons from one side to the other.
Chemical Reactions continued:
- For a chemical reaction to occur, there needs to be the opportunity for two molecules to collide (‘collision theory’).
- The higher the energy of the molecules, the faster they move and the greater chance they have of reacting.
- The minimum energy that is required for a reaction is known as the energy of activation.
- Chemical reactions are reliant on the correct temperature and enough reactants.
- Changes in pressure can also change the speed of reactions, with increasing pressure forcing molecules closer together.
Catalyst & Inhibitors:
- A catalyst speeds up reactions by lowering the activation energy required. Catalysts that the body produces are called ‘enzymes’. For example, consider the enzyme ‘HMG- CoA reductase’ in the production of cholesterol and CoQ10.
- Inhibitors act antagonistically to catalysts. They stop the catalyst from being so effective by making the activation energy higher and hence slow down the reaction time. Many drugs are inhibitors e.g. ‘Statins’ are HMG-CoA reductase inhibitors.
Hydrolysis 🆚 Dehydration synthesis:
Reversible Reactions:
Buffer Systems:
Oxidation and Reduction Reactions:
Antioxidants:
- Antioxidants work by donating an electron to the free radicals to convert them to harmless molecules, without being damaged themselves.
- Antioxidants consist of a group of vitamins, phytochemicals and enzymes that work to neutralise free radicals before they harm our bodies.
- The key to a good antioxidant is that it must be stable once it has given away its electron.
Antioxidants continued:
Hydroxyl group:
- Alcohols – they are polar and hydrophilic.
* Dissolve easily in water.
Sulfhydryl group:
- Common in some protein chains. Found in the sulphur- containing amino acid cysteine.
- Polar and hydrophilic.
Carboxyl group:
- Found in amino acids.
* They are hydrophilic and can interact as a weak acid or as negative particle.
Amine Group:
- Found in amino acids.
* The -NH2 group can act as a weak base if necessary (mopping up H+).
Esters:
• Predominate bond in triglycerides.
Phosphates:
- Found in ATP.
* Phosphate groups are very hydrophilic (dissolve easily in water), as they can form a double negative charge.
Major Carbohydrate Groups:
Isomers:
Disaccharides:
• Two monosaccharides can join together in a dehydration synthesis to from a disaccharide.
– This dehydration reaction occurs by ‘removing water’ to create a ‘glycosidic bond’.
• If we were to ingest a disaccharide, we can break it apart by putting water back into the bond
– this is known as ‘hydrolysis’.
• Lactose constitutes 5% of cow’s milk and 7% of human milk.
• Maltose is formed during the hydrolysis of starch.
• Sucrose is table sugar (glucose and fructose).
Triglycerides:
Saturated (full) Fats:
Monounsaturated Fats (mono=one double bond):
Naming Fatty Acids:
Cis- and Trans- Configurations:
Omega-3 and 6 Fatty Acids:
Omega-3 and 6 Fatty Acids:
Lipoproteins:
Phospholipids:
