Unit 1: Chemistry of Life

Elements. 4 elements used to build biological molecules

Substances that cannot be broken down into simpler substances by chemical means. Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N)

Trace Elements

Elements required by an organism only in very small quantities (e.g. Copper (Cu), Iron (Fe), Iodine (I))

Atoms, Subatomic Particles, and Isotopes

The unit of life and the building blocks of the physical world.

• Protons (+)

• Neutrons (0)

• Electrons (-)

Atoms having the same # of protons but differing in the # of neutrons

Compounds

Consisting of 2+ elements. Held together by chemical bonds (e.g. ionic, covalent, hydrogen)

Ionic and Covalent Bonds

Ionic: Formed b/w 2 atoms when one or more electrons are transferred from one atom to another

Covalent: Formed when electrons are shared b/w atoms

• Non-polar Covalent: Electrons are equally shared

• Polar Covalent: Electrons are unequally shared

Hydrogen Bonds. What are special properties are caused by hydrogen bonding between water molecules?

Weak chemical bonds (compared to ionic & covalent) that form when a hydrogen atom, covalently bonded to a electronegative atom (F, O, N), is attracted to another electronegative atom

• Cohesion, adhesion, surface tension, high heat capacity, expansion on freezing

Cohesion & Adhesion

Cohesion: Tendency to stick to other molecules of the same substance

Adhesion: Tendency to stick to other surfaces

Capillary Action

The movement of water within roots, trunks, and branches due to the forces of adhesion, cohesion, and surface tension

Surface Tension

The property of the surface of a liquid that allows it to resist an external force, due to the cohesive nature of its molecules

Acids & Bases. Results of dissolving them in water?

Acids (<7): Solutions containing hydrogen ions (H+). Dissolving acids in water results in the release of lots of hydrogen ions

Bases (>7): Solution containing hydroxide ions (OH-). Dissolving bases in water results in the release of lots of hydroxide ions

Organic & Inorganic Molecules

Molecules containing a carbon-hydrogen bond

Molecules that don’t contain a carbon-hydrogen bond

Monomers & Polymers

Individual building blocks of a polymer

Chains of building blocks in macromolecules

Dehydration Synthesis (condensation) & Hydrolysis

A water molecule is removed when a covalent bond forms b/w 2 monomers

A water molecule is added when a covalent bond is broken b/w a polymer

4 Macromolecules

Carbohydrates, Lipids, Proteins, Nucleic Acids

Function of carbohydrates

Primary energy source (short & long term)

Function of lipids

Long term energy storage, insulation, protection, cell membrane, signalling molecules

Function of proteins

Basic building blocks of most biological structures. Building, transport, enzymes maintenance, repair, signalling, chem reactions. Energy source

Carbohydrates

Organic compounds that contain C, H, and O in a ratio of approximately 1:2:1. Categorized as either monosaccharides, disaccharides, or polysaccharides.

Monosaccharides

Immediate energy sources for cells (e.g. glucose & fructose). Important part of food. Made by plants during photosynthesis. Have OHs and Hs attached to them.

Disaccharides

When 2 monosaccharides are joined through a bond called a glycosidic linkage (e.g. maltose, sucrose, lactose). Must be broken down into monosaccharides before they can be used.

Polysaccharides

Made up of many repeated units of monosaccharides. Consist of branched (glycogen) or unbranched (cellulose) chains of monosaccharides. Starch can be both branched and unbranched.

Glycogen & Starch

Sugar storage molecules. Glycogen stores sugar in animals. Starch stores sugar in plants

Cellulose

Made up of β-glucose. Major part of the cell wall in plants. Provides structural support

Chitin

A polymer of β-glucose molecules, serving as a structural molecule in the walls of fungus and in the exoskeletons of arthropods

Proteins. Its building blocks and its structure

Important for structure, function, and regulation of tissues and organs.

Amino acids are its building blocks, containing carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

Proteins contain an amino group (–NH2), a carboxyl group (–COOH), a hydrogen, and an R-group

Amino Acid structure. How do aminos differ? What affects whether an amino is more hydrophobic or more hydrophilic?

Contains NH2 (amino group) and COOH (carboxyl molecule). Different amino acids only differ in the R-group. Side chain polarity.

Categories of Amino Acids

Hydrophobic (non-polar and uncharged)

Hydrophilic (polar and uncharged)

Ionic (polar and charged)

Hydrophobic Amino Acids

Do not interact well with water. Side chains non-polar = no significant positive or negative charge. Cluster together in the interior of proteins away from water. E.g. leucine, valine, phenylalanine

Hydrophilic Amino Acids

Interact well with water. Side chains polar. Side chains form hydrogen bonds with water. No electrical charge. Reside on exterior of proteins, close to water. E.g. serine, threonine, asparagine

Ionic Amino Acids

Side chains carry full electrical charge. Donate or accept protons = negative or positive charge. Involved in formation of salt bridges, helping stabilize protein structures.

Physiological pH

pH of human body, around 7.4

Which amino acids are negatively charged at physiological pH? Why?

Glutamic acid and aspartic acid are negatively charged at physiological pH because their carboxyl groups donate protons

Which amino acids are positively charged at physiological pH? Why?

Lysine and arginine are positively charged at physiological pH because their amino groups accept protons

Which two amino acids contain sulfur in their side chains?

Methionine and cysteine contain sulfur in their side chains

What happens when two amino acids join? How?

Form a dipeptide. The carboxyl group of one amino acid combines with the amino group of another amino acid

Peptide Bond

A bond between two amino acids

Polypeptide

Long chain of amino acids linked together by peptide bonds

Primary structure of a protein

Linear sequence of amino acids

What forms when a polypeptide chain twists and folds on itself?

A 3D protein, forming either a coil (alpha helix) or zigzagging pattern (beta-pleated sheets)

Secondary structure of protein

alpha helix and beta-pleated sheets

Tertiary structure

When secondary structure reshapes the polypeptide, amino acids that were far away in primary structure arrangement can now interact with each other

Quaternary structure

Different polypeptide chains interact with each other. E.g. Haemoglobin, 4 separate polypeptide chains interacting with each other

Lipids consists of? Examples of lipids

Carbon (C), hydrogen (H), oxygen (O). Triglycerides, phospholipids, steroids