Chemistry and biochemistry I; the study of the chemical compounds and reactions in living systems Flashcards
Learning outcomes:
- Key concepts in chemistry and biochemistry, including water, pH buffers
- Structure and functions of carbohydrates
- Structural and functions of lipids
Chemistry
The science that deals with the composition and properties of substances and various elementary forms of matter (gas, liquid, solid)
Biochemistry
This science concerned with the chemical and physicochemical processes and substances that occur within living organisms
Bio = life
Matter, what is it and what is it made from?
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 and 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:
o Hydrogen = H
o Carbon = C
o Calcium = Ca
o 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
* It is useful to know some element of abbreviations, for example, in clinic notes (i.e. ‘FE deficiency’) and because it is common in medical texts
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 atom 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 my shells of 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 becomes unpaired
Atoms analogy
“Atoms are Like the 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
The periodic table is a list of all 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)
Each column contains elements that react in a similar way.
* All of the elements in column one react with water. The lower down the column indicate a more vigourous reaction
The Periodic Table: Halogens
A specific column of elements in the periodic table is collectively known as the ‘halogens’.
* Like with any column in the periodic table, the halogens share very similar chemical and physical properties
* In nutrition, this is highly relevant when considering the role of iodine in thyroid health. Recall that iodine is required for the synthesis of thyroid hormones (T3 and T4)
o If present in the body, the other halogens (e.g. fluoride and chlorine ) can enter the thyroid, preventing the formation of T3 and T4 (inducing hypothyroidism)
o Fluoride is in toothpaste, tap water and mouth washes, whilst chlorine is in swimming pools and chlorinated washed vegetables
Counting subatomic particles
- Atomic number = Number of protons
- Mass number = Number of protons + Number of neutrons
- Number of neutrons = mass number number (always bigger) – atomic number
e.g. Potassium (K): - Atomic number = 19
- Mass number = 39.0983
So; - Protons = 19
- Neutrons = 20
- Electrons = 19
Isotopes
Isotopes = atoms of the same element which have a different number of neutrons in the nucleus
* In nature there are often different versions of the same atom called isotopes
* This does not affect the chemical activity of the atom as neutrons have no charge, but it does change the mass
Iso = equal, -topos =- place
Isotopes and Radiation
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.
E.g. 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 with 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 labeled with either radioactive carbon– 14 or nonradioactive carbon– 13. In the subsequent 10 to 30 minutes, the detection of isotype labeled carbon dioxide in exhaled breath indicates that the urea is 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.
Electrons shells
Electrons like to ‘hang out’ in certain numbers (2, 8, 8, 8) so the optimum number of electrons in a shell is a known number
- This means that the first electron shell has 2 electrons, whilst the second 8 and so on
- 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:
1. Ionic bonding – atoms transfer electrons (1 donates, 1 receives)
2. 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 3 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 contains various other minerals too) in
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 are calcium and chlorine have ended up with a full outer shell
Sodium ion
Sodium has one electron in its outer shell
* Energetically its is 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
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
Polar convalent bonds form where electrons are shared and unequally. This happens because some atoms have a lot of ‘electron pulling power’.
- Some elements have lots of protons compare to the number of electrons shells i.e. a strong positive centre. These elements referred to ‘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.
- F, Cl, O and N are the most electronegative elements
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 separate ions. In addition, the different electrical charges in water can allow water molecules to become attracted to other molecules (hence water dissolved salts)
* 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)
Hydro = water, -phillic = loving, -phobic = hating
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, magnesium, phosphate, bicarbonate
* Electrolytes are important body constituents because:
o Conduction of electricity is essential for nerve/muscle function
o They exert osmotic pressure important for water balance
o Some play an important role in acid base balance
Electro = Electric, lyte = from ‘lutos’ meaning released
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 irons in solution. This creates lots of OH-
- Water is a neutral solution because that every H+ released and 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
pH = ‘potential of hydrogen’
Acids and bases: alkaline foods
In a healthy digestive system, the following is the case;
* 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
Acids and bases: acidic foods
- Before consumption, dairy is not very acidic and is also high in calcium, an alkaline mineral. Yet dairy is considered more ‘acidic’ because of the higher proteins/sulphur amino acid content. The sulphur amino acids increase sulphuric acid formation, which and then disrupts blood pH drawing more calcium from bones and increasing calcium lost in urine.
- For this reason meat, also high in sulphur amino acids, will have a net acid effect regardless of whether or not it is organic, since amino acid ratios are identical in both
- Other acidic foods are those rich in refined sugars and processed foods. It is also worth noting that stress and being sedentary also create an acidic environment
Testing pH in the body
Cancer lives in an acidic environment. It is thought that a tissue pH of 8 of above would start to kill cancer cells
* It is vital to consider tissue acidity when considering the ‘terrain’ of the body, i.e. What is the environment
* Given the significant link between body acidity and the effect this has an optimising the environment for various diseases such as cancer, it is vital practitioners are able to measure pH
* Ideally we would measure ‘ tissue pH’ directly, although this is very difficult. The blood will always work hard to maintain its own pH (through breathing, the kidneys and buffer systems) between 7.35–7.45. Therefore, urine and saliva are the good ‘outputs’ of the body to assess.
Using a strip of pH (litmus) paper instructions:
* 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 10 minutes and then spit onto the pH paper.
Remember this gives you information about the terrain/environment. You’re aiming for a slightly alkaline or neutral pH. Many cancer patients do in fact have pH results of 4.5-6. pH is a close reflection of what an individual has eaten.
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 electrons from one side to the other
* E.g. A + B =AB
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 and inhibitors
A catalyst speeds up reactions by lowering the activation energy required
* This means the reaction is faster or can occur at a lower temperature
* 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
Types of Chemical Reactions
Anabolic reactions are synthesis (building) reactions
* This occurs when the body is making new substances and building bonds
* For example, taking amino acids and building a protein. This requires energy
* A + B = AB
Catabolism (catabolic reactions) describes reactions where ‘breaking down’ occurs
* For example, when breaking down food, releasing energy from them. We trap that energy as ‘ATP’.
* AB = A + B
