Chemistry & Biochemistry I Flashcards
(79 cards)
1
Q
What is the definition of „Chemistry”?
A
the science that deals with the composition and properties of substances and various
elementary forms of matter (gas, liquid, solid).
2
Q
What is the definition of “Biochemistry”?
A
the science concerned with the chemical and physicochemical processes & substances that occur within living organisms.
3
Q
What is “matter”?
A
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.
4
Q
Chemical Elements:
A
• 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
5
Q
Elements in the Human Body:
A
- 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.
6
Q
Elements in the Human Body:
A
- 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.
7
Q
Subatomic Particles:
A
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.
8
Q
Electrons:
A
- 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
9
Q
Atoms Analogy:
A
“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.
10
Q
The Periodic Table:
A
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).
11
Q
Halogens ➡️ iodine in thyroid health:
A
- 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.
12
Q
Counting Subatomic Particles:
A
Atomic number = number of protons.
Mass number = number of protons + number of neutrons.
Number of neutrons = Mass number (always bigger) – atomic number.
13
Q
Isotopes:
A
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.
14
Q
Isotopes in Medicine:
A
• 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.
15
Q
Electron Shells:
A
- 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.
16
Q
Hydrogen - The Simplest Atom of All:
A
- 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’.
17
Q
Bonding:
A
- 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.
18
Q
Ionic Bonding:
A
- 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).
19
Q
Ions:
A
- 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.
20
Q
Sodium Ion:
A
- 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+.
21
Q
Covalent Bonds:
A
- 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.
22
Q
Polar Bonds:
A
•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.
23
Q
Hydrogen Bonding:
A
• 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.
24
Q
Water - The Universal Solvent:
A
- 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).
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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.
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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.
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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.
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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.
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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.
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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.
31
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.
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Types of Chemical Reactions:
• Anabolic reactions are synthesis (building) reactions.
– This occurs when the body is making new
substances and building new bonds.
– For example, taking amino acids and building a protein. This requires energy.
– A + B = A - B
• Catabolism describes reactions where “breaking
down” occurs.
– For example, when breaking down food, releasing energy from them. We trap that energy as ‘ATP’.
– A-B = A + B
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Hydrolysis 🆚 Dehydration synthesis:
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Reversible Reactions:
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Buffer Systems:
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Oxidation and Reduction Reactions:
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Free Radicals:
molecules or compounds that have an unpaired electron in their outer shell.
* Free radicals want to stabilise their outer shell, so they try and ‘steal’ electrons from other stable molecules. By doing so, they become destructive, causing ‘oxidation’.
* This leaves the attacked molecule with an unpaired electron, so a chain reaction of oxidative damage occurs. Free radicals can even take electrons from DNA, which can damage genes and can ultimately result in cancerous changes.
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Oxidative Damage:
* Free radicals can cause ‘oxidative damage’ to tissues in the body. Oxidative damage is linked to cancer, atherosclerosis (endothelial damage), fibromyalgia and neurodegenerative diseases.
* Free radicals develop from processes within our bodies such as aerobic respiration, metabolism & inflammation.
* They can also come from the environment, e.g. pollution, sunlight, strenuous exercise, X-rays, smoking, alcohol.
* In a healthy body there are mechanisms in place to “mop up” excess free radicals, but if exposure is high these can become overwhelmed.
* We need to reduce the exposure of our clients to excess sources of free radicals, whilst also optimising their antioxidant status in an effort to protect them from free radical damage.
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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.
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Antioxidants continued:
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Antioxidant Recycling:
• Antioxidants (AO) work best as a collection, where they can recycle each other. They do not work in isolation.
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Biochemical Molecules:
• Living things are characterised by molecules made from carbon.
– Any other groups of atoms that are attached to the carbon skeleton are known as ‘functional groups’.
– Functional groups contribute to the structure and function of that molecule.
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Functional Groups:
*Note: The ‘R’ group is an abbreviation for the unreactive part of the molecule that is just made up of carbon and hydrogen bonds
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Hydroxyl group:
* Alcohols – they are polar and hydrophilic.
| * Dissolve easily in water.
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Sulfhydryl group:
* Common in some protein chains. Found in the sulphur- containing amino acid cysteine.
* Polar and hydrophilic.
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Carboxyl group:
* Found in amino acids.
| * They are hydrophilic and can interact as a weak acid or as negative particle.
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Amine Group:
* Found in amino acids.
| * The -NH2 group can act as a weak base if necessary (mopping up H+).
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Esters:
• Predominate bond in triglycerides.
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Phosphates:
* Found in ATP.
| * Phosphate groups are very hydrophilic (dissolve easily in water), as they can form a double negative charge.
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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.
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Major Carbohydrate Groups:
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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).
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Isomers:
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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).
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Polysaccharides:
* Polysaccharides contain 10s-100s of monosaccharides in glycosidic bonds.
* Typically long chains of glucose molecules joined together e.g. starch, glycogen & cellulose.
* They are normally insoluble in water (because they have given up many –OH groups) and hence starch (e.g. pasta) doesn’t just dissolve in water.
* Polysaccharides do not taste sweet.
* Their digestion begins in the oral cavity.
* The most common type in the body is glycogen.
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Starch: Amylose & Amylopectin
• Starch is the major dietary source of carbohydrate.
• Starch is found in foods such as bread, rice
and pasta. Its digestion begins in the oral cavity.
• Starch is made up of two different polysaccharide components.
– 20-25% Amylose
– 75-80% Amylopectin
• Amylose is a single chain of glucose units.
• Amylopectin is also made from glucose
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Starch: Amylose & Amylopectin
• Amylopectin is highly branched, leaving more surface area available for digestion. It’s broken down quickly, which means it produces a higher rise in blood sugar (glucose) and subsequently, a higher rise in insulin.
• Amylose is a straight chain, which limits the amount of surface area exposed for digestion. Foods high in amylose are sometimes
referred to as sources of resistant starch
as they are digested more slowly.
• Due to its slower digestion, some resistant starch ends up in the large intestine where
it can act as a food source for the bacteria there
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Glycogen:
• Glycogen is a polysaccharide of glucose which functions as the primary short-term energy storage.
• Each glycogen molecule is made up of about 60,000 glucose molecules and has even
more branches that amylopectin.
• It is made and stored primarily by the liver and the muscles.
• Glycogen in the liver can be used to help maintain blood sugar levels.
• Whereas the glycogen in the muscles can only be used by that particular muscle.
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Cellulose:
* Cellulose is the structural material of plants – found in plant cell walls.
* It is also a glucose polymer but the units are linked in a different way using different bonds, giving a flat ribbon-like strand, with an overall rigid structure.
* Humans lack the correct enzymes to break the ‘unique’ bonds between glucose molecules in cellulose, so we cannot digest it.
* Instead, cellulose acts as fibre which assists with the movement of materials through the intestines.
* Cellulose is the single most abundant organic compound on earth.
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Functions of Carbohydrates:
• Energy – carbohydrates are a primary fuel for energy production and also provide a limited storage form of energy, glycogen (i.e. fasting).
• Fibre (cellulose):
– Needed for proper bowel function.
– Protects against cardiovascular disease (14g per 1000kcal).
– Protects against diabetes (15g per day).
– Increase satiety (14-24g per day) & aids weight loss (14g per day).
– Protects against colorectal cancer.
• Glucose can be used for a number of processes, including ATP production, Glycogen synthesis, Triglyceride synthesis (if excess in quantity) & Amino acid synthesis
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Carbohydrate Digestion:
• Salivary amylase starts working on the end of the long glucose chains in starches (hence if you chew starch for a long period, you will start to taste sweetness).
• Salivary amylase works well at a fairly neutral pH, but is deactivated by stomach acid.
• In the small intestine, the pancreas
releases pancreatic amylase which continues
carbohydrate digestion, but this time into disaccharide units.
• The last stage of carbohydrate digestion involves brush border enzymes in the small intestine (lactase, maltase and sucrase). Remember that in pathologies such as coeliac disease, the brush border can be damaged leading to poor carbohydrate digestion.
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Lipids:
* Lipids contain the elements Carbon, Hydrogen and Oxygen, just like carbohydrates, but in a different ratio.
* Lipids have fewer polar -OH groups, so they are hydrophobic.
* To move around the body, they are often bonded to a protein to make them more soluble (proteins act like “taxis”). They are then called ‘lipoproteins’.
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Triglycerides:
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Functions of Triglycerides:
* Fats provide a source of energy, but the process of energy released from fats is less efficient than when carbohydrates are used.
* Fats provide a convenient form in which to store excess calorific intake (extra glucose is also turned into triglycerides).
* Insulation.
* Protection of body parts and organs (e.g. kidneys).
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Saturated (full) Fats:
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Monounsaturated Fats (mono=one double bond):
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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.
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Naming Fatty Acids:
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Cis- and Trans- Configurations:
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Cis- and Trans- Configurations:
• 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. Trans-
fats “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).
• Consider how an oil that keeps being heated becomes thicker as the fatty acids become more linear and hence more solid.
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Essential Fatty Acids:
• Essential fatty acids (or EFAs) are polyunsaturated fatty acids that cannot be constructed within the body from other components and, therefore, must be obtained from the diet.
• There are two families of EFAs:
Omega-3 and Omega-6.
• The body can convert one Omega-3 to another Omega-3, for example, but cannot create an Omega-3 from scratch.
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Omega-3 and 6 Fatty Acids:
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Omega-3 and 6 Fatty Acids:
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Functions of EFAs:
• Fluidity and structure of cell membranes.
• Synthesis of prostaglandins – hormone-like substances responsible
for many functions at cellular level and regulating body processes.
• Regulate oxygen use, electron transportation and energy production.
• Help to form haemoglobin.
• Support the production of digestive enzymes.
• Help make the lubricants for joints.
• Help transport cholesterol in the blood.
• Help generate electric currents and keep the heart rate regular.
• Needed by the tissues of the brain, retina, adrenal glands and testes.
• Help balance the immune system and prevent allergies.
• Ensure proper nerve transmission especially in the brain.
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Oxidation of Fatty Acids (OIL RIG):
• Polyunsaturated fats such as EFAs are very prone to becoming free radicals.
• When these fats are heated, electrons can be lost. This means that a fat is formed
that becomes a free radical. This then further reacts with the oxygen in the air over the cooking pan which becomes even more damaging.
• The CH2 groups between the double bonds are especially vulnerable because radicals formed at these points in the molecule are very stable.
• The damaged fats formed will be incorporated into cell membranes.
• Radical formation is accelerated by light, oxygen and heat.
• Keep polyunsaturated fats in dark glass
bottles in the fridge – never use for cooking!
• To cook with, you should use saturated fats (where there are no vulnerable points for electrons to be stolen), e.g. organic coconut oil (for higher temperatures).
• It is thought that olive oil can be used to cook at lower temperatures because it only has one double bond.
• However, it has been shown that Extra Virgin Olive Oil remains stable when cooked at higher temperatures. This exception is thought to be due to its higher antioxidant content.
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Lipoproteins:
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Types of Lipoprotein:
• Very Low Density Lipoproteins (VLDL)
- carry newly synthesised triglycerides from the liver to adipose tissue (if high: a sign of over-eating).
• Low Density Lipoproteins (LDL)
-carry cholesterol from the liver to cells of the body. Needed to repair cells, support cell membranes and synthesise sex and adrenal hormones.
• High Density Lipoproteins (HDL) - collect cholesterol from the body's tissues, bringing it back to the liver.
• The balance between LDL and HDL is ultimately important.
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Phospholipids:
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Steroids:
* Steroids are lipids that are formed from cholesterol.
* They differ in shape from triglycerides, where they are formed of four rings of carbon atoms joined together at their base.
* Sterols are steroid bases that contain an –OH group.
* Steroids are used to create hormones, e.g. oestrogen, testosterone, cortisol, etc.
* We do not need to eat/ingest cholesterol because the liver can produce it.
