Biochem Ch. 5

Front 1

amino acid residues

Back 1

amino acids making up a protein

Front 2

polypeptides

Back 2

amino acid polymer

Front 3

peptides

Back 3

amino acid polymer with less than 50 amino acids

Front 4

proteins

Back 4

amino acid polymer with more than 50 amino acids

Front 5

amphoteric

Back 5

a molecule being able to behave as an acid or a base

Front 6

zwitterions

Back 6

molecules that bear both positive and negative charges on different atoms

Front 7

nonpolar amino acids

Back 7

glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, cysteine, proline
hydrophobic R groups, important in maintaining 3D protein structure

Front 8

aromatic

Back 8

a class of hydrocarbons that contain cyclic structures with unique properties, unsaturated, hydrophobic

Front 9

aliphatic

Back 9

nonaromatic hydrocarbons, hydrophobic

Front 10

polar amino acids

Back 10

serine, threonine, tyrosine, asparagine, glutamine
hydrophilic R groups hydroxyl or amide

Front 11

acidic amino acids

Back 11

aspartate, glutamate
carboxylate group on R, negative at physiological pH

Front 12

basic amino acids

Back 12

lysine, arginine, histidine
positive charge at physiological pH, all have nitrogen-related R groups

Front 13

other roles of amino acids

Back 13

1. chemical messengers
2. precursors to a variety of complex N-containing molecules
3. metabolic intermediates

Front 14

neurotransmitters

Back 14

substances released from one nerve cell that influence the function of a second nerve cell or a muscle cell

Front 15

hormones

Back 15

chemical signal molecules produced in one cell that regulate the function of other cells

Front 16

asymmetric/ chiral carbons

Back 16

carbons with four different groups bonded to it

Front 17

stereoisomers

Back 17

molecules that differ only in the spatial arrangement of their atoms

Front 18

enantiomers

Back 18

two molecules that are mirror images of each other due to different spatial arrangement
have identical properties except for rotating polarized light in opposite directions

Front 19

optical isomers

Back 19

molecules that are otherwise identical except for rotating polarized light in opposite directions

Front 20

dextrorotatory

Back 20

+, rotates polarized light in the clockwise direction

Front 21

levorotatory

Back 21

-, rotates polarized light in the counterclockwise direction

Front 22

primary stereoisometric form found in living things

Back 22

primarily L

Front 23

icoelectric point

Back 23

the pH at which a molecule has no net charge

Front 24

peptide bonds

Back 24

amide linkages formed when the unshared electron pair of the alpha-amino nitrogen atom of one amino acid attacks the alpha-carboxyl carbon of another in a nucleophilic acyl substitution reaction

Front 25

N-terminal

Back 25

amino acid in a polypeptide that has the free amino group. written on the left

Front 26

C-terminal

Back 26

amino acid in a polypeptide that has the free carboxyl group. written on the right

Front 27

disulfide bridge

Back 27

bond between two sulfide groups on two cysceines
help stabilize many polypeptides

Front 28

Schiff bases

Back 28

imine product of the reaction when amine groups react reversibly with carbonyl groups

Front 29

aldimines

Back 29

Schiff bases formed from reactions between amino groups and aldehyde groups

Front 30

functions of proteins

Back 30

catalysis, structure, movement, defense, regulation, transport, storage, stress response

Front 31

heat shock proteins

Back 31

proteins that promote the correct refolding of damaged proteins

Front 32

multifunction proteins

Back 32

proteins that can perform multiple, often unrelated, functions

Front 33

protein families

Back 33

classification of proteins based on amino acid sequence and similarities in 3D structure. Proteins are thought to share a common ancestry

Front 34

superfamilies

Back 34

classification of proteins that are more distantly related

Front 35

fibrous proteins

Back 35

shape classification with long, rod-shaped molecules that are insoluble in water and physically tough
often function as structural or protective proteins

Front 36

globular proteins

Back 36

shape classification with compact, spherical molecules that are usually water-soluble
dynamic functions

Front 37

simple protein

Back 37

proteins that contain only amino acids

Front 38

conjugated protein

Back 38

simple proteins combined with a nonprotein component

Front 39

prosthetic group

Back 39

nonprotein component of a conjugated protein

Front 40

apoprotein

Back 40

a conjugated protein without its prosthetic group

Front 41

holoprotein

Back 41

a conjugated protein with its prosthetic group

Front 42

glycoproteins

Back 42

conjugated proteins with a carbohydrate prosthetic group

Front 43

lipoproteins

Back 43

conjugated proteins that contain lipid molecules

Front 44

metalloproteins

Back 44

conjugate proteins that contain metal ions

Front 45

phosphoproteins

Back 45

conjugate proteins that contain phosphate groups

Front 46

hemoproteins

Back 46

conjugate proteins that contain heme groups

Front 47

primary structure

Back 47

amino acid sequence of a protein

Front 48

secondary structure

Back 48

partial folding of a polypeptide showing certain localized arrangements of adjacent amino acids

Front 49

tertiary structure

Back 49

overall 3D shape of a polypeptide

Front 50

quaternary structure

Back 50

proteins that consist of two or more polypeptide chains

Front 51

homologous

Back 51

describes proteins with similar amino acid sequences that have arisen from the same ancestral gene

Front 52

molecular diseases

Back 52

diseases caused by mutations in protein folding

Front 53

alpha-helix

Back 53

common secondary structure formed when a polypeptide chain twists into a right-handed helical conformation. H bonds occur between the N-H of each amino acid and the carbonyl carbon four amino acids away. R groups stick out form the helix.

Front 54

beta-pleated sheet

Back 54

common secondary structure formed when two or more polypeptide chain segments line up side by side. Stabilized by hydrogen bonds that form between polypeptide backbone N-H and carbonyal groups of adjacent chains. May be parallel or antiparallel.

Front 55

supersecondary structures/ motifs

Back 55

patterns of alpha-helix and beta-pleated sheet structures within a protein

Front 56

protein folding

Back 56

a process in which an unorganized, nascent molecule acquires a highly organized structure

Front 57

fold

Back 57

the core 3D structure of a domain of a large globular protein

Front 58

domain

Back 58

typically structurally independent segments that have specific functions in large globular proteins

Front 59

modular proteins

Back 59

eukaryotic proteins that contain numerous duplicate or imperfect copies of one or more domains that are linked in series

Front 60

hydrophobic interactions

Back 60

stabilizes tertiary structure as hydrophobic R groups are forced together away from water as well as expelling water from inside the protein, increasing entropy, making the action favorable

Front 61

electrostatic interactions

Back 61

stabilizes tertiary structure via interactions between groups of opposite charge. Strongest are between ionic groups. Can only occur in absence of water.

Front 62

salt bridges

Back 62

noncovalent bonds in protein folding

Front 63

ligands

Back 63

signal molecule

Front 64

subunit

Back 64

one polypeptide chain within a protein that contains more than one

Front 65

hydrogen bonds

Back 65

stabilizes tertiary structure by forming hydrogen bonds within a protein or on the surface.

Front 66

covalent bonds

Back 66

stabilizes tertiary structure by chemically linking structures. Disulfide bride most prominent. Important for protecting the protein from changes in pH or salt concentration.

Front 67

hydration

Back 67

stabilizes tertiary structure formed from structured water around the protein.

Front 68

oligomers

Back 68

multisubunit proteins in which some or all subunits are identical

Front 69

protomers

Back 69

a component of an oligomer; may consist of one or more subunits

Front 70

allostery

Back 70

the control of protein function through ligand binding

Front 71

allosteric transitions

Back 71

ligand-induced conformational changes so that the protein's affinity for other ligands is altered

Front 72

effectors/modulators

Back 72

ligands that trigger allosteric transitions

Front 73

intrinsically unstructured proteins (IUPs)

Back 73

unstructured proteins

Front 74

natively unfolded proteins

Back 74

proteins with a complete lack of ordered structure

Front 75

denaturation

Back 75

the process of structure disruption, which may or may not involve protein unfolding

Front 76

causes of denaturation

Back 76

changes in pH via strong acids or bases, alters H bonds
organic solvents disrupt hydrophobic interactions
detergents disrupt hydrophobic interactions
reducing agents break disulfide bridges and disrupt H-bonds and hydrophobic interactions
increased salt concentration disrupts the solvation sphere
heavy metal ions disrupt salt bridges and bind with sulfhydryl groups
temperature increase disrupts weaker interactions
mechanical stress disrupts interactions

Front 77

amphipathic

Back 77

molecules containing both hydrophobic and hydrophillic components

Front 78

site-directed mutagenesis

Back 78

a recombinant DNA technique in which specific sequence changes can be introduced into a predetermined position in cloned genes

Front 79

circular dichromism

Back 79

a type of spectroscopy in which the relationship between molecular motion and structure is probed with electromagnetic radiation

Front 80

molten globule

Back 80

a partially organized globular state of a folding polypeptide that resembles the molecule's native state

Front 81

molecular chaperones

Back 81

molecules that aid in the folding of polypeptides by protecting primary structure from inappropriate interactions and ensuring quick precise folding

Front 82

hsp70s

Back 82

a family of molecular chaperones that bind to and stabilize proteins during the early stages of folding

Front 83

hsp60s or chaperonins

Back 83

a family of molecular chaperones which mediate protein folding by forming a hollow protein complex with a hydrophobic interior

Front 84

aldol condensation

Back 84

a reaction in which two aldehydes form an alpha, beta-unsaturated aldehyde linkage

Front 85

cooperative binding

Back 85

a mechanism in which binding of one ligand to a target molecule promotes the binding of other ligands.