AP Biology Unit 1: Chemistry of Life

Water

Water

A polar molecule. Its polarity allows it to form hydrogen bonds. It contains covalent bonds between the oxygen and hydrogen atoms, with oxygen having a high electronegativity while hydrogen has a low electronegativity, making the electrons in the covalent bond between the two elements unequally shared. This results in a polar covalent bond, with a partial negative charge around the oxygen and a partial positive charge around the hydrogen.

Hydrogen Bond

When the partial negative charge on an oxygen atom in one water molecule is attracted to the partial positive charge on a hydrogen atom in another water molecule.

Polar

When electrons are shared, but not equally due to differences in electronegativity.

Nonpolar

When the sharing of electrons between atoms is equal.

Covalent Bond

A link between two atoms where electrons are shared.

Electronegativity

The ability of an atom to attract shared electrons in a covalent bond.

Adhesion

The property of water that lets water molecules stick to another surface.

Cohesion

The property of water that lets water molecules stick to each other.

Adhesion and Cohesion

Adhesion and Waters high surface tension and ability to climb up the xylem in plants through capillary action are given to it by this?

Waters High Specific Heat

As a result of water's ability to form hydrogen bonds, more energy is required to separate water molecules during phase changes, giving water this.

Moderating Climate

Due to water's high heat capacity, it can absorb and release large amounts of energy, stabilizing climates in locations near large bodies of water.

Expanding upon Freezing

Since water can form hydrogen bonds, there is more space between water molecules in the solid state than in the liquid state, so ice has a lower density than liquid water and floats on water, having profound consequences for organisms in ponds or lakes that freeze. The layer of ice helps protect the organisms below from temperature extremes in the atmosphere, increasing their chances of surviving the winter. If ice were denser than liquid water, the ice would sink, leaving the remaining water in the lake exposed and vulnerable to more freezing and increasing the chance that the lake would freeze solid during the winter, resulting in fewer organisms in the lake surviving.

Acting as a Great Solvent

Water has a partially positive and negative end, so it can readily dissolve ionic compounds and other polar molecules.

pH

Measures the concentration of H+ ions in a solution.

Neutral

A pH of 7.

Acid

A pH less than 7.

Base

A pH greater than 7.

pH of a Water-Based Solution

Depends on how many of the water molecules are dissociated and the relative number of these ions. Pure water will dissociate and produce equal concentrations of H+ ions and OH- ions, resulting in a pH of 7. Acids increase the relative concentration of H+ ions in a solution, and bases increase the relative concentration of OH- ions in a solution.

Buffer

Can form acids or bases in response to changing pH levels in a cell. They can absorb excess H+ or OH- ions to maintain a steady pH in a solution.

Biological Macromolecules

A large, organic molecule such as carbohydrates, lipids, proteins, and nucleic acids which are primarily made of six elements: nitrogen, carbon, hydrogen, oxygen, phosphorus, and sulfur.

Carbon

The backbone of macromolecules. It has four valence e- and is extremely versatile in the way it can bond to other atoms; it can form single, double, or triple bonds. It can form linear, branched, or ring-type structures. It is found in all types of macromolecules.

Oxygen

Has six valence e- and typically forms two bonds. It is found in all types of macromolecules.

Sulfur

Has six valence e- and typically forms two bonds. It is typically found in proteins.

Nitrogen

Has five valence e- and typically forms three bonds. It is found in nucleic acids and proteins.

Phosphorus

Has five valence e- and typically forms three bonds. It is found in nucleic acids and some lipids.

Hydrogen

Has one valence e- and forms a single bond. It is found in all types of macromolecules.

Monomers

A basic molecule that can covalently bond to other monomers to form long chains called polymers.

(Building Blocks)

Polymers

Long molecules consisting of similar/identical building blocks linked by covalent bonds.

Dehydration Synthesis

A reaction that synthesis/joins two molecules together, resulting in a loss of water.

Hydrolysis

A reaction that adds water molecules to break the bonds between monomers.

Carbohydrates

Polymers of sugar monomers. The types of sugars used to make it and how they are linked determines the structure and function of it. The sugars may be joined in linear structures or in branched chains. It can be used to store energy (like in starch or oxygen) and can have structural functions (like in cellulose). The type of linkages between the sugars in it that store energy is different from the type of linkages found in it that have a structural function.

Lipids

Nonpolar macromolecules that function in energy storage, cell membranes, and insulation. One of its building blocks is fatty acids. How it functions in a cell is dependent on the its saturation level.

Saturated Fats

Fatty acids with the max number of C-H single bonds which are solid at room temp and usually originate in animals.

Unsaturated Fats

Fatty acids with at least one C=C double bond which are liquid at room temp and usually originate in plants.

Ester Bonds

Occurs in fats and lipids between a carboxyl group (-COOH) and the carbon chain by the elimination of a water molecule.

Phospholipids

A lipid built from a glycerol molecule, two fatty acids, and a phosphate group. Because the fatty acids are nonpolar and the phosphate is polar, they are amphipathic.

Amphipathic

Having both hydrophobic and hydrophilic regions.

Hydrophobic

A molecule that repels water.

Hydrophilic

A molecule that is attracted to water.

Steroids

Relatively flat, nonpolar molecules. Many are formed by modifying cholesterol molecules. Examples include estradiol, testosterone, and cortisol

Triglycerides

Three fatty acids with their carboxyl end bound to glycerol via an ester bond/linkage.

Ester Bond/Linkage

A bond that occurs in fats and lipids between a carboxyl group and the carbon chain.

Glycerol

A short 3-carbon chain that is often used to bind different fatty acids together and form lipid structures.

Nucleic Acids

(DNA and RNA). Polymers of nucleotides. The genetic info is stored and communicated through the order of these nucleotides.

Nucleotides

A unit of the DNA or RNA molecule with a five-carbon sugar (deoxyribose and ribose), a nitrogenous base (adenine, thymine, cytosine, guanine, or uracil), and a phosphate group. They have directionality in that the phosphate group is always attached to the 5’ carbon in the sugar, and the 3’ carbon always has a hydroxyl group to which new ones may be added.

Proteins

Polymers of amino acids. They are formed when amino acids join through peptide bonds. They function in enzyme catalysis, maintaining cell structures, cell signaling, cell recognition, and more.

Amino Acids

They have an amino group, a carboxylic acid group, a hydrogen atom, and a side chain (R-group) attached to a central carbon. The R-group is unique for each of these; it determines its identity and whether it will be nonpolar, polar, acidic, or basic.

Primary Structure

Amino acids are joined by peptide bonds and the resulting polypeptide chains have directionality, with an amino (NH2) terminus and a carboxyl (COOH) terminus. The order of the amino acids in the polypeptide chain determines this structure of the protein. A change in this structure may have severe effects on the function of the protein, as seen in sickle cell disease.

Peptide Bonds

Covalent bonds that hold together amino acids.

Polypeptide Chains

Chains/linear sequences of amino acids.

Secondary Structure

Once the primary structure is formed, hydrogen bonds may form between adjacent amino acids in the polypeptide chain, driving the formation of this structure, which includes alpha helixes and beta-pleated sheets..

Tertiary Structure

The three-dimensional folded shape of the protein, often determined by the hydrophobic/philic interactions between R-groups in the polypeptide. The most stable will have hydrophilic R-groups on the surface of the protein (in contact with the watery environment of the cells cytosol), while the amino acids with hydrophobic R-groups will be in the interior of the protein (away from the watery cytosol). They may also include disulfide bridges between sulfur atoms.

Chaperonins

Special proteins that help fold a polypeptide into its three-dimensional structure.

Quaternary Structure

Connects the subunits of proteins with multiple polypeptide chains so the protein can function as a unit.

DNA

Five-Carbon Sugar - Deoxyribose

Nitrogenous Bases - Adenine, thymine, cytosine, and guanine

Strands - Double-stranded helix

Function - Holds genetic info

Location - Usually found in the nucleus

RNA

Five-Carbon Sugar - Ribose

Nitrogenous Bases - Adenine, uracil, cytosine, and guanine

Strands - Usually single-stranded but can form three-dimensional structures when folded

Function - Transcribes and regulates the expression of genetic info

Location - Found in both the nucleus and the cytoplasm

Pyrimidines

The nitrogenous bases of thymine, uracil, and cytosine. They complement purines.

Purines

The nitrogenous bases of adenine and guanine. They complement pyrimidines.

Thymine and Adenine

Forms two hydrogen bonds with one another.

Guanine and Cytosine

Forms three hydrogen bonds with one another.