Unit 1 - Chemistry of Life

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.