Unit 1 - Chemistry of Life

Matter

Anything that takes up space and has mass

Element

A substance that cannot be broken down into other substances by chemical reactions

Compound

A substance consisting of two or more different elements combined in a fixed ratio

Essential Elements

of the 92 naturally occurring elements 20-25% are essential to survive and reproduce. CHOPN make up 96% of living matter

Trace Elements

of the 92 naturally occurring elements, these are required by an organism in very small quantities

Octet Rule

elements will gain, lose, or share electrons to complete their valence shell and become stable (like noble gases)

Chemical Bonds

an attraction between two atoms, resulting from the sharing or transferring of valence electrons

Electronegativity

the measure of an atom’s ability to attract electrons to itself

Covalent bonds

when two or more atoms share electrons (usually between two nonmetals)

Nonpolar Covalent

Electrons are shared equally between two atoms

Polar Covalent

Electrons are not shared equally between two atoms

Ionic Bonds

The attraction between oppositely charged atoms (ions); Usually between a metal and nonmetal (metal transfers electrons to nonmetal); Forms ionic compounds and salts; Occurs when there is a transfer of electrons from one atom to another atom forming ions

Cation

positively charged ion

Anion

negatively charged ion

Hydrogen Bonds

the partially positive hydrogen atom in one polar covalent molecule will be attracted to an electronegative atom in another polar covalent molecule

Intermolecular Bond

bond that forms between molecules

Polarity

polar covalent bonds created by unequal sharing of electrons between oxygen and hydrogen within the molecule of water

Cohesion

attraction of molecules for other molecules of the same kind (H2O to H2O); Hydrogen bonds between H2O molecules hold them together and increase cohesive forces

Adhesion

the attraction to other molecules that are polar or have charge (H2O to other molecules)

Capillary Action

the upward movement of water due to the forces of cohesion, adhesion, and surface tension

High Specific Heat

H2O resists changes in temperature; Heat must be absorbed to break hydrogen bonds, but heat is released when hydrogen bonds form

High heat of vaporization

Water requires a large amount of energy to evaporate due to strong hydrogen bonds

Evaporative cooling

as water molecules evaporate, the surface they evaporate from gets cooler

Density

as water solidifies it expands and becomes less dense

Solvent

dissolving agent in a solution; Water is a versatile solvent; Its polar molecules are attracted to ions and other polar molecules it can form hydrogen bonds with

pH

a measure of how acidic or basic (alkaline) a solution is; Water can dissociate into hydrogen (H+) and hydroxide ions (OH-)

Acid

substance that releases hydrogen ions (H+) when dissolved in water

Base

substance that accepts H+ OR releases hydroxide ions (OH-) when dissolved in water

Buffer

a solution that resists changes in pH when an acid or base is added

Organic chemistry

the study of compounds with covalently bonded carbon

Organic compounds

compounds that contain carbon and hydrogen

Carbon

can form single, double, or triple covalent bonds; A single carbon can form up to four covalent bonds!; Can form LONG chains; Most commonly formed with hydrogen, oxygen, and nitrogen; Carbon can use its valence electrons to form covalent bonds to other carbons; Carbon chains form the skeletons of most organic molecules

Functional groups

chemical groups attached to the carbon skeleton that participate in chemical reactions

macromolecules

molecules made of smaller subunits

Polymers

chain like macromolecules of similar or identical repeating units that are covalently bonded together

Monomers

the repeating units that make up polymers

Dehydration reaction

bonds two monomers with the loss of H2O

Hydrolysis

breaks the bonds in a polymer by adding H2O

Carbohydrates

Includes sugars and polymers of sugars; Contain a carbonyl group and many hydroxyl groups; Comprised of C, H, and O; Monosaccharides: simple sugars

Disaccharides

two monosaccharides joined together by covalent bonds

Polysaccharides

polymer with many sugars joined via dehydration reactions

Storage polysaccharides

Plants store starch (polymer of glucose monomers); Allows plants to store excess glucose

Animals store glycogen (polymer of glucose); Stored in liver and muscle cells

Structural polysaccharides

Cellulose: tough substance that forms plant cell walls

Chitin: forms exoskeleton of arthropods

Formation of Proteins

Amino acids to peptides to polypeptides to proteins

Protein

molecule consisting of polypeptides (polymers of amino acids) folded into a 3D shape; Comprised of C, H, O, N, and S; Shape determines function

Amino Acids

Molecules that have an amino group and a carboxyl group; 20 different ones with each a unique side chain that determine physical and chemical properties

Polypeptides

many AA linked by peptide bonds; Each polypeptide has a unique sequence of AAs and directionality

Function of Proteins

Antibody-help protect the body from disease; Enzyme- carry out chemical reactions or assist in creating new molecules; Messenger- transmit signals (ie hormones)'; Structural- provide structure and support; Transport/storage- bind to and carry small atoms and molecules through the body

Primary Protein Structure

Linear chain of AA; Determined via genes; Dictates secondary and tertiary forms

Secondary Protein Structure

Coils and folds due to hydrogen bonding within the polypeptide backbone

Tertiary Protein Structure

3D folding due to interactions between the side chains of the AAs; Reinforced by hydrophobic interactions and disulfide bridges of the side chains; The covalent bond formed between sulfur atoms of two cysteine monomers

Quaternary Protein Structure

Association of two or more polypeptides; Found in only some proteins

Nucleic Acids

polymers made of nucleotide monomers; Function to: Store, transmit and express hereditary information

Nucleotides

Contain 3 parts: Nitrogenous base, Five carbon sugar (pentose), Phosphate group(s)

Nitrogenous Base

Two types, pyrimidines and purines, that are essential components of nucleotides, playing a crucial role in the encoding of genetic information.

Pyrimidines

one ring with 6 atoms

Cytosine, Thymine, Uracil

Purines

one ring with 6 atoms bonded to one ring with 5 atoms

Adenine, Guanine

Five Carbon Sugar

A sugar is bonded to the base; In DNA the sugar is deoxyribose; In RNA the sugar is ribose

Phosphate Group

A phosphate group is added to the 5’ carbon of the sugar (which is attached to the base) to form a nucleotide

Polynucleotides

Phosphate groups link adjacent nucleotides; Phosphodiester linkage; Directionality 5’ to 3’; The sequence of bases along the DNA or mRNA is unique for each gene

DNA

Consists of two polynucleotides; Forms a double helix; Strands are antiparallel; Held together by hydrogen bonds between bases: Cytosine binds to guanine and Adenine binds to thymine

RNA

Single stranded polynucleotide; Variable in shape; Due to base pairing within RNA: Adenine bonds to uracil and Cytosine bonds to guanine

Lipids

class of molecules that do not include true polymers; Generally small in size; Often not considered to be a macromolecule; nonpolar-hydrophobic

Fats

composed of glycerol and fatty acids via ester linkage

Glycerol

classified as an alcohol (hydroxyl groups)

Fatty acids

long carbon chains (carboxyl group at one end)

Saturated fatty acid

no double bonds between carbons in the carbon chain = more hydrogen (think: saturated with hydrogen)

Unsaturated fatty acid

contains one or more double bonds

Phospholipids

Major component of cell membranes; Two fatty acids attached to a glycerol and a phosphate; Assemble as a bilayer in H2O where Tails are hydrophobic and Head is hydrophilic

Steroids

Lipids that have four fused rings; Unique groups attached to the ring determine the type