Unit 1 Biochemistry and cell structure

• All substances are made from atoms of elements.
• Molecules are made from two or more atoms.
• If the atoms in the molecule are the same, then the molecule is that of an element.
• Fibrous proteins have a structural role in the body.
• The high number of hydrogen bonds between the polypeptide chains in collagen stops the chains sliding past each other and makes collagen strong.
• Examples of proteins with quaternary structure are shown in the diagram below.
• If the atoms are different, then the molecule is a compound.
• Ions can be formed from metals, non-metals, or combinations of elements.
• Ions can be positively charged – they have lost one or more electrons and have more protons than electrons, which is why they have a positive charge.
• Ions can be negatively charged – they have gained one or more electrons and have more electrons than protons, which is why they have a negative charge.
• Compounds are made from atoms of two or more elements and can include metals and non-metals (ionic compounds) or just non-metals (molecular compounds).
• Particles with a charge (ions or polar molecules) have different properties from molecules with no charge (non-polar).
• Ions and polar compounds attract oppositely charged particles and play important roles in the structure of molecules.
• Non-polar compounds do not dissolve in water but will dissolve in lipids (fats/oils) – they are said to be lipid-soluble.
• The six most common elements, accounting for 99% of the mass of the human body are oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.
• Carbon, hydrogen and oxygen are the main components of all organic molecules.
• Found in amino acids/nucleic acids.
• Calcium strengthens teeth, bones and nerves in animals, and cell walls in plants.
• Phosphorus is present in cell membranes/ATP/nucleic acids.
• The remaining 1% of the mass of the human body is made of about 10 other elements, mainly: potassium, sulfur, chlorine, sodium, magnesium, iron, copper, manganese, zinc, and iodine.
• Most of these key elements are found as inorganic ions.
• Organic compounds always contain the elements carbon and hydrogen, and many contain oxygen and/or nitrogen.
• Carbohydrates, lipids, proteins are examples of biochemicals.
• Water is the most abundant compound in any organism (about 60-70% of the fresh mass of a human).
• Water is essential as all biochemical reactions take place in aqueous solution i.e., dissolved in water.
• Water is a polar molecule – it has no overall charge, but the hydrogen atoms have a partial positive charge and the oxygen atoms have a partial negative charge.
• A water molecule is usually drawn using solid lines for the bonds between the hydrogen and oxygen atoms.
• The partial charges are shown as δ+, delta positive and δ−, delta negative.
• Many globular proteins have a metabolic function in organisms, for example, enzymes, antibodies, and hormones.
• The secondary structure of a protein can be alpha helix or beta pleated sheet.
• Proteins with a secondary structure play important structural roles in organisms.
• Disulfide bridges are strong and more difficult to break, a higher temperature or more extreme pH would be needed to break these bonds.
• Beta pleated sheets form layers of protein, for example, fibroin in silk.
• Additional hydrogen bonds can also form between polar variable groups.
• The amino acid at the NH2 end – the N terminal – will have a basic group at the end, while the amino acid at the COOH end – the C terminal – will have an acidic group.
• These are insoluble in water and have a structural function in organisms, for example, α-keratin in wool and collagen in skin and blood vessels.
• Ionic bonds are formed from charged variable groups and can interact with water, which helps a protein to dissolve.
• These make the amino acid chain fold and twist into a new shape, which is called the secondary structure of the protein.
• The tertiary structure of a protein or polypeptide depends on the properties of the R groups.
• Hydrophobic interactions take place when the variable groups are non-polar, they are repelled by water and are usually found on the inside of the protein as far away from water as possible; a protein rich in non-polar side groups will be less soluble in water.