BIOC 3621 exam 1

functional groups

groups of atoms that give rise to the characteristic reactions of organic compounds

monomers

small molecules that may bond to many others to form a polymer

polymers

macromolecules formed by the bonding of smaller units

proteins

macromolecules formed by the poymerization of amino acids

nucleic acids

macromolecules formed by the polymerization of nucleotides

catalytic activity

the ability to increase the rate of a chemical reaction

catalysis

the process of increasing the rate of chemical reactions

genetic code

the information for the stucture and function of all living organisms

genome

the total DNA of the cell

genes

indivdual units of inheritance

prokaryotes

microorganisms that lack a distinct nucleus and membrane-enclosed organelles

eukaryotes

organisms whose cells have a well-defined nucleus and membrane-enclosed organelles

organelle

a membrane-enclosed portion of a cell with a specific function

ribosomes

the sites of protein synthesis in all organisms, consisting of RNA and protein

cell membrane

the outer membrane of the cell that separates it from the outside world

cell wall

the outer coating of bacterial and plant cells

chloroplasts

organelles that are the sites of photosynthesis in green plants

nucleus

the organelle that contains the main genetic apparatus in eukaryotes

nucleolus

a portion of the nucleus rich in RNA

chromatin

a complex of DNA and protein found in eukaryotic nuclei

chromosomes

linear structures that contain the genetic material and associated proteins

mitochondrion

an organelle that contains the apparatus responsible for aerobic oxidation of nutrients

cristae

folds in the inner mitochondrial membrane

matrix

the part of a mitochondrion enclosed within the inner mitochondrial membrane

endoplasmic reticulum

a continuous single-membrane system throughout the cell

golgi apparatus

a cytoplasmic organelle that consists of flattened membranous sacs, usually involved in secretion of proteins

lysosomes

membrane-enclosed organelles that contain hydrolytic enzymes

peroxisomes

membrane-bounded sacs that contain enzymes incolved in the metabolism of hydrogen peroxide

glyoxysomes

membrane-enclosed organelles that contain the enzymes of the glyoxylate cycle

cytosol

the portion of the cell that lies outside the nucleus and the other membrane-enclosed organelles

cytoskeleton

a lattice of fine strands, consisting mostly of protein, that pervades the cytosol

vacuoles

cavities within the cytoplasm of a cell, typically enclosed by a single membrane, that may serve secretory, excretory, or storage functions

endosymbiosis

a symbiotic relationship in which one organism lives inside the body or cell of another organism

reduction

the gain of electrons

oxidation

the loss of electrons

thermodynamics

the study of transformations and transfer of energy

spontaneous

in thermodynamics, characteristic of a reaction or process that takes place without outside intervention

free energy

a thermodynamic quantity; diagnostic for the spontaneity of a reaction at constant temperature

exergonic

energy-releasing

endergonic

energy-absorbing

equilibrium

a state in which opposing forces or influences are balanced.

enthalpy

a thermodynamic quantity measured as the heat of reaction at constant pressure

electronegativity

a measure of the tendency of an atom to attract a bonding pair of electrons

polar bonds

bonds in which two atoms have an unequal share in the bonding electrons

nonpolar

refers to a bond in which two atoms share electrons evenly

dipoles

molecules with positive and negative ends due to an uneven distribution of electrons in bonds

salt bridge

an interaction that depends on the attraction of unlike charges

van der Waals forces

Noncovelant associations between moelcues. Weak attraction that occur between molecues that demonstrate low levels of polarity.

van der Waals radius

the distance between an atom's nucleus and its effective electronic surface

London dispersion forces

an attraction between transient induced dipoles

Hydrophilic

tending to dissolve in water

hydrophobic

tending not to dissolve in water

hydrophobic interactions

attractions between molecules that are nonpolar

amphipathic

refers to a molecule that has one end with a polar, water-soluble group and another end with a nonpolar hydrocarbon group that is insoluble in water

hydrogen bonding

a noncovalent association formed between a hydrogen atom covalently bonded to one electronegative atom and a lone pair of electrons on another electronegative atom

acid strength

the tendency of an acid to dissociate to a hydrogen ion and its conjugate base

acid dissociation constant

a number that characterizes the strength of an acid

ion product constant for water

a measure of the tendency of water to dissociate to give hydrogen ion and hydroxide ion

Henderson-Hasselbalch equation

pH = pKa + log [A-]/[HA]

a mathematical relationship between the pKa of an acid and the pH of a solution containing the acid and its conjugate base

titration

an experiment in which a measured amount of base is added to an acid

equivalence point

the point in a titration where an acid is exactly neutralized

buffer solution

a solution that resists changes in pH on addition of moderate amounts of strong acid or strong base

zwitterions

molecules that have both a positive and a negative charge

side chain group

the portion of an amino acid that determines its identity

stereochemistry

the branch of chemistry that deals with the three-dimensional shape of molecules

chiral

refers to an object that is not superimposable on its mirror image

achiral

refers to an object that is superimposable on its mirror image

Stereoisomers

molecules that differ from each other only in their configuration

L and D amino acids

amino acids whose stereochemistry is the same as the stereochemical standards L- and D-glyceraldehyde, respectively

Electrophoresis

a method for separating molecules on the basis of the ratio of charge to size

isoelectric pH (pI)

The pH at which a molecule has no net charge; also known as the isoelectric point

peptide bond

an amide bond between amino acids in a protein

peptides

molecules formed by linking two to several dozen amino acids by amide bonds

polypeptide chain

the backbone of a protein; it is formed by linking amino acids by peptide (amide) bonds

native conformation

three-dimensional shapes of proteins with biological activity

primary structure

the order in which the amino acids in a protein are linked by peptide bonds

secondary structure

the arrangement in space of the backbone atoms in a polypeptide chain

tertiary structure

the arrangement in space of all the atoms in a protein

quaternary structure

the interaction of several polypeptide chains in a multisubunit protein

alpha helix

one of the most frequently encountered folding pattern in the protein backbone

beta pleated sheet

one of the most important types of secondary structure, in which the protein backbone is almost fully extended with hydrogen bonding between adjacent strands

beta bulge

a common nonrepetitive irregularity in beta-sheets

reverse turns

parts of proteins where the polypeptide chain folds back on itself

fibrous proteins

proteins whose overall shape is that of a long, narrow rod

globular proteins

protein whose overall shape is more or less spherical

X-ray crystallography

an experimental method for determining the three-dimensional structure of molecules, such as the tertiary or quaternary structure of proteins

heme

an iron-containing cyclic compound found in cytochromes, hemoglobin, and myoglobin

denaturation

the unraveling of the three-dimensional structure of a macromolecule caused by the breakdown of noncovalent interactions

dimers

molecules consisting of two subunits

trimers

molecules consisting of three subunits

tetramers

molecules consisting of four subunits

chaperone proteins

assist in folding other proteins