Chapter 3 Vocabulary

Front 1

Chemical Evolution

Back 1

The theory that states that simple chemicals came together to form larger, more complex ones. The complexity continued until it formed life.

Front 2

Oparin-Haldane Proposal

Back 2

1. The reactions of H2, N2, NH3, and CO2 led to more complex componds

2. Simple organic compounds came together to form larger molecules (i.e. amino acids, nucleotides, and sugars).

3. Further complexity adds to create proteins, nucleic acids, and complex carbohydrates.

4. Life became possible when one of these complex molecules could self-replicate.

Front 3

Scientific Theory

Back 3

A well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method and repeatedly tested and confirmed through observation and experimentation.

Front 4

Prebiotic (Primordial) Soup Model

Back 4

Typically in reference to the early oceans, ponds, lakes, or any body of water where small molecules reacted with others in close contact with organic compounds.

Front 5

Proteins

Back 5

A macromolecule consisting of one or more polypeptide chains composed of 50 or more amino acids linked together. Each protein has a unique sequence of amino acids. Usually refers to the complete, often functional form.

Front 6

Amino Acids

Back 6

The simple sub-unit of a protein.

Front 7

Side Chain

Back 7

Another name for the R-group.

Front 8

R-group

Back 8

Unique structure of an amino acid (20 different kinds). Properties of amino acids vary because of the R-group. Attached to alpha carbon.

Front 9

Functional group

Back 9

A group of atoms responsible for the characteristic reactions of a particular compound. In amino acids this is in reference to either the amino, carboxyl, or special R- group.

Front 10

Amino group

Back 10

NH2

Front 11

Carboxyl group

Back 11

-COOH

Front 12

Sulfhydryl group

Back 12

Located on R-group. Can form disulfide (S--S) bonds between other sulfhydrl groups.

Front 13

Hydroxyl group

Back 13

Usually relates to polarity of the amino acid.

Front 14

Hydrophobic

Back 14

Do not interact with water. Amino acids that are nonpolar usually have a lot of carbon boded to hydrogen, and few have sulfur. Tendency to clump together in water.

Front 15

Hydrophilic

Back 15

Polar or charged side chains interact readily with water. Contains a oxygen on the R-group or some charged atom.

Front 16

Polar

Back 16

A molecule containing a partial positive and partial negative charge on either side.

O--H

N--H

Front 17

Nonpolar

Back 17

A bond where electrons are equally shared.
C--H

Front 18

Monomer

Back 18

A single sub unit. Examples include amino acids, nucleotides, or a sugar. For proteins this is just a single amino acid.

Front 19

Polymer

Back 19

More than one monomer bound together. For proteins this involves polymerization of amino acids.

Front 20

Polymerization

Back 20

The process by which small monomers are covalently bonded together to form polymers.

Front 21

Macromolecules

Back 21

Very large molecules that are made of smaller ones that are joined together in a chain.

Front 22

Oligopeptide (Peptide)

Back 22

Fewer than 50 amino acids linked together.

Front 23

Polypeptide

Back 23

50 or more amino acids linked together.

Front 24

Endergonic

Back 24

Referring to a chemical reaction that requires the input of energy to occur, where the products are greater free energy than the reactants.

Front 25

Exergonic

Back 25

Referring to the release of energy or increasing entropy.

Front 26

Condensation reaction (dehydration reaction)

Back 26

A chemical reaction in which two molecules are joined covalently with the removal or water as a byproduct.

Front 27

Hydrolysis

Back 27

The reverse of condensation reactions, here polymers are broken by adding water. The resulting monomer is separated from a polymer.

Front 28

Peptide bond

Back 28

In a protein polymer it is the amino group bonded to the carboxl group through a condensation reaction.

Front 29

Residue

Back 29

Refers to a specific monomer in the polypeptide chain.

Front 30

N-terminus

Back 30

The starting of a polypeptide chain where there is a "free" amino group.

Front 31

C-terminus

Back 31

The tail of a polypeptide chain where there is a "dangling" carboxyl group.

Front 32

catalysis

Back 32

Something that speeds up a reaction, but is not used up in the process.

Front 33

enzyme

Back 33

A protein catalyst used by living organisms to speed up and control biological reactions.

Front 34

Primary structure

Back 34

A complete polypeptide chain.

Front 35

Secondary structure

Back 35

Folding of primary structure held together by H-bonds.

Front 36

Alpha helix

Back 36

A type of secondary structure of proteins that is coiled. Held by H-bonds.

Front 37

Beta pleated sheets

Back 37

A type of secondary structure of proteins where segments fold in 180 degree bends that also fold in planes.

Front 38

Tertiary structure

Back 38

Further complexity of secondary structures of proteins where the R-groups interact with other R-groups or the back-bone of the peptide itself.

Front 39

Van der Waals interactions

Back 39

A temporary partial charge interactions that involve the hydrophobic R-groups of a peptide. Associated with tertiary structures.

Front 40

Disulfide bonds

Back 40

Form between two cysteines through a reaction between the sulfhydryl groups. Associated with tertiary structures.

Front 41

Quaternary structures

Back 41

multiple polypeptides that come together in a particular arrangement. Involves multiple tertiary structures acting as one.

Front 42

Dimer

Back 42

A chemical compound composed of two identical or similar monomers.

Front 43

Tetramer

Back 43

A polymer containing four identical monomers.

Front 44

Multienzyme complex

Back 44

A structurally distinct and ordered collection of enzymes, often catalyzing successive steps in a metabolic pathway.

Front 45

Denaturation

Back 45

Unraveling of protein structure by some external stress (strong acid/base, organic solvent)

Front 46

Renaturation

Back 46

The refolding of a protein to its native form. Only few proteins can do this.

Front 47

Molecular Chaperone

Back 47

A protein that facilitates the folding of newly synthesized proteins into their correct shape. Uses ATP in the process.

Front 48

Prion

Back 48

Proteins that are incorrectly folded and result in an infectious, disease causing agent. Can lack nucleic acids.

Front 49

Substrates

Back 49

A reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction.

Front 50

Lock-and-Key model.

Back 50

The interaction between a substrate and enzymes where the fit determines if the reaction takes place.

Front 51

Active Site

Back 51

The place where substrates bind and interact. This is where catalysis actually take place.