4. Chemistry of life

Chemistry of life

• Elements
• Subatomic Particles
• Compounds
• Water: The Versatile Molecule
• Acids and Bases
• Organic Molecules

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Elements

• Elements: are substances that cannot be broken down into simpler substances by chemical means.
• Oxygen (O), carbon (C), hydrogen (H), and nitrogen (N).
• These four elements are used to build biological molecules, such as carbohydrates, proteins, lipids, and nucleic acids. They are also used to form storage compounds and cells in all organisms.
• Some elements are known as trace elements because they are required by an organism only in very small quantities. They include iron (Fe), iodine (I), and copper (Cu).
• Other elements are present but in smaller quantities.

Subatomic Particles

• Atoms are the unit of life and are the building blocks of the physical world.
  • Protons are positively charged (+) particles
  • Neutrons are uncharged particles.
  • Electrons are negatively charged (–) particles
• Some atoms have the same number of protons but differ in the number of neutrons in the nucleus. These are called isotopes.

Compounds

• Consists of two or more elements
• The atoms of a compound are held together by chemical bonds, which may be ionic bonds, covalent bonds, or hydrogen bonds.
• An ionic bond is formed between two atoms when one or more electrons are transferred from one atom to the other.
• The charged forms of the atoms are called ions.
• A covalent bond is formed when electrons are shared between atoms. If the electrons are shared equally between the atoms, the bond is called non-polar covalent. If the electrons are shared unequally, the bond is called polar covalent.

Water: The Versatile Molecule

• Hydrogen bonds are weak chemical bonds that form when a hydrogen atom that is covalently bonded to one electronegative atom is also attracted to another electronegative atom.
• The hydrogen bonds that hold water molecules together contribute to a number of special properties, including cohesion, adhesion, surface tension, high heat capacity, and expansion on freezing.
• Water molecules have a strong tendency to stick together. This exhibits cohesive forces.
• Water molecules also like to stick to other substances—This makes them adhesive
• These two forces taken together—cohesion and adhesion—account for the ability of water to rise up the roots, trunks, and branches of trees. This is capillary action.
• The cohesion of water molecules contributes to another property of water known as surface tension. The surface of the water has tension to it. The water molecules are stuck together, and light things like leaves and water striders can sit atop the surface without sinking.

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ACIDS AND BASES

• Reactions are also influenced by whether the solution in which they occur is acidic, basic, or neutral.
• A solution is acidic if it contains a lot of hydrogen ions (H+). If you dissolve an acid in water, it will release a lot of hydrogen ions.
• Bases do not release hydrogen ions when added to water. They release a lot of hydroxide ions (OH–).
• The acidity or alkalinity of a solution can be measured using a pH scale. The pH scale is numbered from 1 to 14. The midpoint, 7, is considered neutral pH.
• The concentration of hydrogen ions in a solution will indicate whether it is acidic, basic, or neutral.
  • pH = –log [H+]
• The pH scale is logarithmic and represents a tenfold change in hydrogen ion concentration.

ORGANIC MOLECULES

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• Molecules with carbon are organic molecules and molecules that do not contain carbon atoms are called inorganic compounds.

• Carbon is important for life because it is a versatile atom, meaning that it has the ability to bind not only with other carbons but also with a number of other elements including nitrogen, oxygen, and hydrogen

• Polymers are chains of building blocks in macromolecules

• Monomers are the individual building blocks of a polymer

• Polymers are formed through dehydration synthesis (or condensation) reactions. A water molecule is lost in the reaction, and a larger compound is formed.

• Hydrolysis is when polymers can also be broken down into monomers.

• The water breaks the bond between the two monomers.

• Four classes of organic compounds central to life on Earth:

1. carbohydrates
2. %%proteins%%
3. @@lipids@@
4. ^^nucleic acids^^

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Carbohydrates

• Carbohydrates are organic compounds that contain carbon, hydrogen, and oxygen. They are in a ratio of approximately 1:2:1
• Most carbohydrates are categorised as either monosaccharides, disaccharides, or polysaccharides. The term saccharides means “sugar.” The prefixes refer to the number of sugars in the molecule.

Monosaccharides:

• It is an energy source for cells.
• The two most common sugars are glucose and fructose. Their chemical formula is C6H12O6
• Glucose is an important part of the food we eat, and it is the product made by plants during photosynthesis.
• Glucose and fructose can be depicted as either “straight” or “rings.” They have OHs and Hs attached to them.

Disaccharides

• When two monosaccharides are joined, the bond is called a glycosidic linkage, and the resulting sugar is called a disaccharide. The disaccharide formed from two glucose molecules is maltose.
• To break up the disaccharide and form two monosaccharides - Just add water.

Polysaccharides

• Polysaccharides are made up of many repeated units of monosaccharides.
• They can consist of branched or unbranched chains of monosaccharides. Need to know for the test : starch, cellulose, and glycogen.
• Glycogen and starch are sugar storage molecules. Glycogen stores sugar in animals and starch stores sugar in plants.
• Cellulose, on the other hand, is made up of β-glucose and is a major part of the cell walls in plants. Its function is to lend structural support.
• Chitin, a polymer of β-glucose molecules, serves as a structural molecule in the walls of fungus and in the exoskeletons of arthropods.

Proteins

• Proteins are important for structure, function, and regulation of your tissues and organs.
• Amino acids are building blocks of proteins. They contain carbon, hydrogen, oxygen, and nitrogen atoms. There are 20 different amino acids.
• Proteins have four important parts around a central carbon:
  • An amino group (–NH2), a carboxyl group (–COOH), a hydrogen, and an R-group.
• Amino acids differ only in the R-group, which is also called the side chain.
• When it comes to spotting an amino acid, look for the amino group (NH2), then look for the carboxyl molecule (COOH).
• Side chain polarity affects whether an amino acid is more hydrophobic or more hydrophilic.
• The AP Exam divides them into 3 broad categories: hydrophobic (non-polar and uncharged), hydrophilic (polar and uncharged), and ionic (polar and charged).

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• Of the common amino acids:

  • Two (glutamic acid and aspartic acid) donate a proton, making them negatively charged.
  • Two (lysine and arginine) accept a proton at physiological pH, which makes them positively charged.

• Two contain the atom sulphur: methionine and cysteine.

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%%Polypeptides%%

• When two amino acids join, they form a dipeptide. The carboxyl group of one amino acid combines with the amino group of another amino acid.
• The bond between two amino acids is peptide bond.
• If a group of amino acids is joined together in a “string,” the resulting organic compound is called a polypeptide. Once a polypeptide chain twists and folds on itself, it forms a 3D structure called a protein.
• The linear sequence of the amino acids is the primary structure of a protein.
• When the polypeptide begins to twist it begins forming either a coil (known as an alpha helix) or zigzagging pattern (known as beta-pleated sheets). These are secondary structures.
• When the secondary structure reshapes the polypeptide, amino acids that were far away in the primary structure arrangement can now also interact with each other. This is called the tertiary structure.
• When different polypeptide chains sometimes interact with each other, they form a quaternary structure. Haemoglobin is a molecule in the blood that helps distribute oxygen to the tissues in the body. It is formed when four separate polypeptide chains interact with each other and is a quaternary structure.

@@Liplids@@

• This consists of carbon, hydrogen, and oxygen atoms.
• The most common examples of lipids are triglycerides, phospholipids, and steroids.
• Lipids are important due to their non-polar structures, they function as structural components of cell membranes, sources of insulation, signalling molecules, and a means of energy storage.
• Triglycerides Our bodies store fat in tissue called, adipose, which is made of cells called adipocytes; these cells are filled with lipids called triglycerides.
• Each triglyceride is made of a glycerol molecule (also called the glycerol backbone) with three fatty acid chains attached to it. A fatty acid chain is covered in hydrogen. One end of the chain has a carboxyl group.
• A fatty acid can be saturated with hydrogens along its long carbon chain or it can’t be unsaturated. If there is a double bond in the chain it is an unsaturated fatty acid.
• Lipid Saturation:The extent of saturation in a lipid can affect its structure and function. The more double bonds that exist within a lipid, the more unsaturated it is.

@@Phospholipids@@

• Phospholipids contain two fatty acid “tails” and one negatively charged phosphate “head”.
• Phospholipids are important because of some unique properties they possess, especially with regard to water.
• The two fatty acid tails are hydrophobic. The reason for this is that fatty acid tails are non-polar, and non-polar substances don’t mix well with polar ones, such as water.
• The phosphate “head” of the lipid is hydrophilic, meaning that it does mix well with water since it carries a negative charge, and this charge draws it to the positively charged end of a water molecule.
• A phospholipid has both a hydrophilic region and a hydrophobic region which makes it is an amphipathic molecule.

@@Cholesterol@@

• Cholesterol is a four-ringed molecule that is found here and there in membranes.
• It generally increases membrane fluidity, except at very high temperatures. Cholesterol is also important for making certain types of hormones and for making vitamin D.

^^Nucleic Acids^^

• They contain carbon, hydrogen, oxygen, and nitrogen and phosphorus. Nucleic acids are molecules that are made up of simple units called nucleotides.
• DNA contains the hereditary “blueprints” of all life. RNA is essential for protein synthesis.

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