Biochemistry 1 Flashcards
Chemistry
the science that deals with the composition and properties of substances and various elementary forms of matter (gas, liquid, solid)
Biochemistry
the science concerned with the chemical and physicochemical processes & substances that occur within living organisms
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
An element
substance made up of just one type of atom so it cannot be split up into simpler substances.
- 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.
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 electron = electric that ‘buzz’ around the outside of the nucleus, neutron = neutral 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 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
The Periodic Table is 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).
The Periodic Table: Halogens
A specific column of elements in the Periodic Table are 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 & T4).
- 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 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 (always bigger) – atomic number.
Isotopes
Isotopes = atoms of the same element which have a different numbers 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.
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.
Electron 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 has 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
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.
types of bonding
- 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.
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
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
Polar covalent bonds form where electrons are shared unequally.
This happens because some atoms have a lot of ‘electron pulling power’.
- 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
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
An acid is a substance that releases a high amount of H+ ions when dissolved in water.
Bases
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 (H2 O), 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).
Acids and Bases
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.
- 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.
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 protein/sulphur amino acid content. The sulphur amino acids increase sulphuric acid formation, which then disrupts blood pH drawing more calcium from bones and increasing calcium loss 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.
pH in the Body
Cancer thrives in an acidic environment. It is thought that a tissue pH of 8 or above would start to kill cancer cells.
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.
You are 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 in electrons from one side to the other.
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.
Hydroxyl group
Sulfhydryl group
Hydroxyl group
- Alcohols – they are polar and hydrophilic.
- Dissolve easily in water.
Sulfhydryl group
- Common in some protein chains. Found in the sulphurcontaining amino acid cysteine.
- Polar and hydrophilic.
Carboxyl group
Amine Group
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 -NH 2 group can act as a weak base if necessary (mopping up H+ ).
Esters
Phosphates
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.
Carbohydrates
Carbohydrates include starches (bread, pasta etc.), cellulose (plants) and sugars.
- All carbohydrates are made of C-H-O.
- The carbon atoms are normally arranged in a ring with oxygen and hydrogen atoms attached.
- Carbohydrates have many -OH groups so they can form hydrogen bonds. This means the smaller carbohydrates such as simple sugars can dissolve easily in water.
- Carbohydrates are grouped into 3 classes, depending on their size: monosaccharides, disaccharides & polysaccharides.
Monosaccharides
Monosaccharides are simple sugars that can exist as single molecules, e.g. glucose and fructose.
- Most monosaccharides have a sweet taste – fructose is the sweetest.
- Monosaccharides are grouped into families named after the number of carbon atoms.
- The names of monosaccharides all end in –ose.
– Triose (3 carbons).
– Pentose (5 carbons).
– Hexoses (6 carbons) e.g. glucose & fructose.
– Heptose (7 carbons).
Isomers
Isomers have the same chemical formula but different structures.
- Analogy: Each atom is a Lego brick. The same number of Lego bricks can be used to create different structures, e.g. a house or a car.
- E.g. C6 H12 O 6 is the formula for fructose, glucose, galactose and mannose.
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
Triglycerides are the main form of dietary fat.
- Contain a single glycerol molecule and three fatty acid chains (these can be saturated or unsaturated – this combination will determine whether its solid or liquid at room temperature).
- Fatty acids are attached to glycerol by a dehydration synthesis reaction and the bond formed is known as an ‘ester’ (different from the glycosidic bond seen in carbohydrates).
- They are broken down by a hydrolysis reaction (like with carbohydrates).
Saturated Fats
- Saturated fats contain single covalent bonds between each of the fatty acid carbon atoms.
- Each carbon atom is saturated with hydrogen atoms.
- Saturated fatty acids are very straight, meaning they can line up close to each other and hence are more likely to be solid. Saturated fats are generally solid at room temperature
- E.g. coconut oil.
Monounsaturated Fats
Monounsaturated fats contain fatty acids with one double covalent bond between two carbons.
- The double bond forces the molecule into a bent configuration.
- Monounsaturated fats are generally liquids at room temperature because the molecules can’t pack very closely together.
- E.g. olive oil.
Polyunsaturated Fats
- Polyunsaturated fats contain more than one double bond in the carbon chain.
- These molecules are ‘kinked’ so they, too, are liquids at room temperature.
- E.g. Sunflower oil, rapeseed oils, vegetable oils.
Fatty Acids
Fatty acids are named according to the closest double bond to the end of the chain.
• The end of the chain is always the end without the oxygens.
– Omega-3 - the double bond is three carbons up from the end.
– Omega-6 - the double bond is 6 carbons up from the end.
• Omega 3 and 6 are essential in our diet.
Cis- and Trans- Configurations
The presence of a double bond means that two different molecular configurations are possible.
– A cis configuration is when the H atoms are on the same side of the double bond.
– A trans configuration is when the H atoms are on separate sides the double bond.
• In nature, nearly all fats have a cis- structure.
Our body recognises these and can use them.
- When we try to create these fats in laboratories/industry, they position the H atoms on opposite sides where they have more space.
- Consider eating sunflower seeds (i.e. from nature) v. eating something cooked in sunflower oil.
- A cis- fatty acid is bent, whereas a trans- fatty acid is more linear.
- Cis- and trans- fats have different properties, especially when incorporated into biological structures such as cell membranes. Cis- fats make cell membranes more flexible. Transfats “stiffen” cell membranes and are prone to oxidative damage and making cell membranes leaky.
- Cis- fats can be turned into trans- fats by heating to high temperatures or heating oil repeatedly (the hydrogen spins around).
- They are also formed during hydrogenation reactions used to make processed foods and margarine (trans-fat).
Omega-3
Omega-3 fatty acids:
- α-linolenic acid (ALA) essential in the diet.
- Eicosapentaenoic acid (EPA).
- Docosahexaenoic acid (DHA)
- Omega-3 fats include:
- ALA – flax seeds, walnuts, green leafy vegetables.
- EPA & DHA – oily fish.
