1.1 - Elements, Compounds, Atoms and Ions

• Matter - anything that has mass and takes up space.

• Element - Matter in its simplest form

• Atom - the smallest form of an element that still displays particular properties.

• Ion - An atom with a negative or positive charge.

• Cation - ion with positive charge; composed of more protons than electrons.

• Anion - ion with negative charge; composed of more electrons than protons.

• Elements can be combined to form molecules. For eg: An oxygen molecule.

• Compounds - molecules that are composed of more than one element. For eg: H2O.

• Organic compounds - contain carbon and usually hydrogen; Inorganic compounds do not.

• Functional Groups - The groups responsible for the chemical properties of organic compounds.

• Amino group: Has the following formula:

• The symbol R stands for “rest of the compound: to which this NH2 group is attached. Example: amino acid. Animes - Compounds containing amino groups; act as bases, and can pick up protons from acids.

• Carbonyl group: Contains two structures:

  

• If the C=O is at the end of a chain, it is an aldehyde. Otherwise, it is a ketone.

• A carbonyl group makes a compound hydrophilic (water-loving, reacting well with water) and polar (a molecule that has an unequal distribution of charge, which creates a positive and negative side to the molecule).

• Carboxyl group: Has the following formula:

• Carboxyl group: A carbonyl group that has a hydroxide in one of the R spots and a carbon chain in the other.

• Shows up along with amino groups in amino acids.

• Act as acids because they are able to donate protons to basic compounds.

• Compounds containing carboxyl groups are known as carboxylic acids.

• Hydroxyl group: Has the following formula:

• Present in compounds called alcohols.

• Polar and hydrophilic like carbonyl groups.

• Phosphate group: Has the following formula:

• Vital components of compounds that serve as cellular energy sources: ATP, ADP and GTP.

• Acidic, like carboxyl groups.

• Sulfhydryl group: Has the following formula:

• Present in the amino acids methionine and cysteine, assists in structure stabilization in many proteins.

1.2 - Water

• Inorganic compound consisting of one oxygen molecule covalently bonded to two hydrogen bonds.

• Electrons shared between the hydrogen and oxygen molecules are closer to the oxygen molecule due to its electronegativity.

• Results in the oxygen molecule being negatively charged and the hydrogen molecule being positively charged.

• Water molecules - polar because they have a positive and negative side.

• Non Polar molecules - neutral charge due to equal sharing of electrons.

• Hydrogen bonding - the attraction between a positively charged hydrogen atom and any other electronegative atom (eg: oxygen).

• May form between atoms within the same molecule or between two separate molecules.

• Water molecule - contains slightly positive charged hydrogens and slightly negative oxygen molecules, allowing it to form up to two hydrogen bonds with other water molecules, leading to a variety of properties unique to water.

  Properties of Water

• Cohesion

• Water molecules linking together due to hydrogen bonds

• Surface tension - the surface of water is difficult to break or stretch.

• Adhesion

• A water molecule is attracted to other substances due to hydrogen bonds.

• The adhesion of water to plant cell walls by hydrogen bonds help counter the pull of gravity in plants.

• Evaporative cooling

• The surface of an object becomes cooler during evaporation as a result of water absorbing energy in the form of heat.

• Evaporation of sweat from the skin of humans lowers body temperature.

• Surface tension

• Surface tension allows water to be resistant to external forces, due to the cohesive nature of water molecules to one another instead of the surrounding molecules in the air.

• Universal solvent

• Water dissolves more substances than any other liquid of Earth.

Structure of a hydrogen bonda. Hydrogen bond between two water molecules.b. Hydrogen bond between an organic molecule (n-butanol) and water

1.3 - Macromolecules

Monomers and Polymers

• Macromolecules - made of single units called monomers that are joined together by covalent bonds to form large polymers, such as carbohydrates, nucleic acids and proteins.

• Due to their large size, lipids are also classified as macromolecules even though they lack the repeating monomer subunits seen in the other molecules.

• Macromolecules - assembled via dehydration synthesis (A reaction that forms a covalent bond between two monomer units while releasing a water molecule in the process).

• Hydrolysis the process by which the covalent bonds between monomer units are broken by the addition of water.

Making and breaking macromolecules

• a. Biological macromolecules are polymers formed by linking monomers together through dehydration reactions. This process releases a water molecule for every bond formed.

• b. Breaking the bond between subunits involves hydrolysis, which reverses the loss of a water molecule by dehydration.

  Lipids

• Organic compounds used by cells as long term energy stores or building blocks.

• Hydrophobic and insoluble in water as they contain a hydrocarbon tail of CH2S that is nonpolar and repellant to water.

• The most important lipids - fats, oils, steroids, and phospholipids.

  

• Fats - lipids made by combining glycerol and three fatty acids - used as long term energy stores in cells.

• Not as easily metabolized as carbohydrates, but are a more effective means of storage. For eg: one gram of fat provides twice the energy of one gram of carbohydrates.

• Saturated fat molecules contain no double bonds; Unsaturated fat molecules contain one or more double bonds, meaning they contain fewer hydrogen molecules per carbon than do saturated fats.

• Fat is formed when three fatty-acid molecules connect to the OH groups of the glycerol molecule. These connecting bonds are formed by dehydration synthesis reactions.

• Steroids - lipids composed of four carbon rings.

• Example - cholesterol, an important structural component of cell membranes that serves as a precursor molecule for another important class of steroids: the sex hormones (testosterone, progesterone, and estrogen).

• Phospholipid - lipid formed by combining a glycerol molecule with two fatty acids and a phosphate group.

• Phospholipids - amphipathic structures - they have both a hydrophobic tail (a hydrocarbon chain) and a hydrophilic head (the phosphate group)

• Major component of cell membranes; hydrophilic phosphate group - forms the outside portion, hydrophobic tail - forms the interior of the wall.

• Structure of phospholipid

  

• Bilayered structure of phospholipids

  

• Carbohydrates

• Simple sugars or complex molecules containing multiple sugars.

• Used by the cells of the body in energy-producing reactions and as structural materials.

• Have the elements C, H, and O. Hydrogen and oxygen are present in a 2:1 ratio.

• Main types of carbohydrates - monosaccharides, disaccharides, and polysaccharides.

• Monosaccharide - simple sugar, the purest form of a carbohydrate. (glucose - C6H12O6)

• Monosaccharides with five carbons (C5H10O5) are used in compounds such as genetic molecules (RNA) and high-energy molecules (ATP).

• Disaccharide - sugar consisting of two or more monosaccharides bound together.

• Common disaccharides - sucrose, maltose, and lactose.

• Sucrose, a major energy carbohydrate in plants, is a combination of fructose and glucose; maltose, a carbohydrate used in the creation of beer, is a combination of two glucose molecules; and lactose, found in dairy products, is a combination of galactose and glucose.

• Polysaccharide carbohydrate containing three or more monosaccharide molecules.

• Usually composed of hundreds or thousands of monosaccharides, act as a storage form of energy, and as structural material in and around cells.

• The most important carbohydrates for storing energy - starch and glycogen.

• Starch - made solely of glucose molecules linked together, is the storage form of choice for plants.

• Animals store much of their carbohydrate energy in the form of glycogen, often found in liver and muscle cells. Glycogen is formed by linking many glucose molecules together.

• Two important structural polysaccharides - cellulose and chitin.

• Cellulose - a compound composed of many glucose molecules, used by plants in the formation of their cell walls.

• Chitin - an important part of the exoskeletons of arthropods such as insects, spiders and shellfish.

• Proteins

• Compound composed of chains of amino acids.

• Functions in the body — serve as structural components; transport aids, enzymes, and cell signals.

• An amino acid consists of a carbon center surrounded by an amino group, a carboxyl group, a hydrogen, and an R group.

• R stands for rest of the compound, which provides an amino acid’s unique personal characteristics; Acidic amino acids have acidic R groups, basic amino acids have basic R groups, and so forth.

• Structure of an amino acid

  

• Amino acid structure exhibiting peptide linkage

  

• Structures of proteins

• Primary structure - the order of amino acids that make up the protein

• Secondary structure - three-dimensional arrangement of a protein caused by hydrogen bonding at regular intervals along the polypeptide backbone.

• Tertiary structure - three-dimensional arrangement of a protein caused by interaction among the various R groups of the amino acids involved.

• Quaternary structure - the arrangement of separate polypeptide subunits into a single protein. Not all proteins have a quaternary structure; many consist of a single polypeptide chain.

• Fibrous proteins - proteins with only primary and secondary structure

• Globular proteins - proteins with only primary, secondary, and tertiary structures

• Either fibrous or globular proteins may contain a quaternary structure if there is more than one polypeptide chain.

1.4 - Nucleic Acids

DNA Structure and Function

• Deoxyribonucleic acid (DNA) - composed of four nitrogenous bases: adenine, guanine, cytosine, and thymine.

• Adenine and guanine - a type of nitrogenous base called a purine, contain a double ring structure.

• Thymine and cytosine - a type of nitrogenous base called a pyrimidine, contain a single-ring structure.

• Scientists James D. Watson and Francis H.C. Crick - given credit for realizing that DNA was arranged in what they termed a double helix composed of two strands of nucleotides held together by hydrogen bonds.

• Adenine always pairs with thymine (A=T) held together by two hydrogen bonds; guanine always pairs with cytosine (C≡G) held together by three hydrogen bonds.

• Each strand of DNA consists of a sugar-phosphate (sugar - deoxyribose) backbone that keeps the nucleotides connected with the strand.

• Purine-pyrimidine bonds

  

• The two strands of a DNA molecule run antiparallel to each other; the 5′ end of one molecule is paired with the 3′ end of the other molecule, and vice versa.

• The 5’ and 3’ ends in DNA structure.

  

RNA Structure and Function

• RNA - Ribonucleic acid.

• Similarities between DNA and RNA - both have a sugar-phosphate backbone; both have four different nucleotides that make up the structure of the molecule.

• RNA’s nitrogenous bases - adenine, guanine, cytosine, and uracil**.**

• Sugar in RNA - ribose.

• While DNA exists as a double strand, RNA is a single-stranded entity.

• Three main types of RNA (all of which are formed from DNA templates in the nucleus of eukaryotic cells) - messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

1.5 - pH: Acids and Bases

• The pH scale - used to indicate how acidic or basic a solution is.

• It ranges from 0 to 14; 7 is neutral.

• Anything less than 7 is acidic; anything greater than 7 is basic.

• The pH scale is a logarithmic scale; a pH of 5 is 10 times more acidic than a pH of 6.

• As the pH of a solution decreases, the concentration of hydrogen ions in the solution increases, and vice versa.

• Chemical reactions in humans function at or near a neutral pH; exceptions - the chemical reactions involving some of the enzymes of the digestive system.