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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

configuration

A

arrangement of atoms around a chiral center

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2
Q

conformation

A

arrangement of atoms in space

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3
Q

isomers

A

2 different chemical compounds which have the same chemical composition but are physically distinct and separable

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4
Q

anomers

A

a chiral center which was not initially present in a molecule but was created by intramolecular bonding

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5
Q

epimers

A

2 stereoisomers which differ only in one chiral center

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6
Q

alpha helix

A

a type of secondary structure commonly found in proteins which is characterized by 3.6 residues per turn and a phi angle of -57 degrees and a psi angle of -47 degrees for a right handed helix and a phi angle of 57 degrees and a psi angle of 47 degrees for a left handed helix

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7
Q

alanine

A

an amino acid with an aliphatic or methyl side chain functional group (Ala) [A]

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8
Q

amino acid

A

a biomolecule; an amino group, a carboxylic acid group, a proton and another functional group attached to the same carbon = an alpha amino carboxylic acid

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9
Q

amphibolic

A

a metabolic pathway which has the characteristics of both catabolism and anabolism

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10
Q

anabolism

A

a metabolic pathway which consumes energy (ATP) to synthesize biomolecules

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11
Q

arginine

A

an amino acid with a guanidinium side chain functional group (Arg) [R] {pka 12.5}

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12
Q

asparagine

A

an amino acid with an amide side chain functional group (Asn) [N]

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13
Q

assay

A

an analytical procedure in which the amount or concentration of an unknown is determined by comparing its response or reaction to that obtained with a known amount or contrition of the same or similar material

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14
Q

beta sheet

A

a type of secondary structure commonly found in proteins which is characterized by 2 linear strands of the polypeptide backbone laying side by side connected with hydrogen bonds and which is characterized by a phi angle of -119 degrees and a psi angle of 113 degrees for parallel beta sheets and a phi angle of -139 degrees and a psi angle of 135 degrees for anti-parallel beta sheets.

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15
Q

biochemistry

A

the science of the molecules and chemical reactions of life

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16
Q

buffer

A

a solution of a weak acid or base which is present in acid-base pair which resists changes in pH when another acid or base is added

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17
Q

carbohydrate

A

polyhyroxyl ketones or polyhydroxyl aldehydes and their derivatives

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18
Q

catabolic

A

a metabolic pathway which produces energy (ATP)

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19
Q

chaotropic agent

A

chaos creating agents– molecules which denature biomolecules (e.g. urea, guanidium, SDS)

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20
Q

chemical isomers

A

2 different molecules which have the same chemical composition

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21
Q

chiral center

A

a single atom or a group of atoms when the attached groups are interchanged the two molecules are not superimposable

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22
Q

chromatography

A

a technique of separation and/or analysis which is based on the relative affinity of solutes for a moving and stationary phases

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23
Q

cooperativity

A

occurs when a change in one parameter influences the change in similar parameters

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24
Q

cysteine

A

an amino acid with a thiol or sufhydral side chain functional group (Cys) [C] {pka 8.4}

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25
Q

denaturation

A

the process by which a biomolecule loses its biological function

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26
Q

diastereomers

A

stereoisomers which contain more than one chiral center but are not mirror images of each other

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27
Q

domain

A

a substructure of the tertiary structure that can evolve, function, and exist independently of the rest of the protein chain

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28
Q

electrophoresis

A

a technique of separation based on the movement of charged molecules in the presence of an electric field

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29
Q

enantiomer

A

2 stereoisomers in which all chiral centers are switched

30
Q

enthalpy

A

the measure of the amount of heat within a system under constant pressure

31
Q

entropy

A

the measure of the disorder of a system

32
Q

free energy (Gibbs)

A

the amount of energy available to do chemical work

33
Q

glutamate

A

an amino acid with a carboxylic acid side chain functional group (Glu) [E] {pka 4.1}

34
Q

glutamine

A

an amino acid with an amide side chain functional group (Gln) [Q]

35
Q

glycine

A

an amino acid with a hydrogen side chain functional group (Gly) [G]

36
Q

histidine

A

an amino acid with an imidazole side chain functional group (His) [H] {pka 6.0}

37
Q

isoelectric focusing

A

a type of electrophoresis in which the gel contains a pH gradient so that the molecules move to the pH location which matches their isoelectric point

38
Q

isoelectric point

A

the pH at which a molecule is electrically neutral or has zero net charge

39
Q

isoleucine

A

an amino acid with a branched aliphatic side chain functional group (Ile) [I]

40
Q

leucine

A

an amino acid with a branched aliphatic side chain functional group (Leu) [L]

41
Q

lipid

A

biomolecules which are insoluble or partially soluble in water and usually extractable by organic (non polar) solvent

42
Q

lysine

A

an amino acid with a primary amine side chain functional group (Lys) [K] {pka 10.5}

43
Q

macromolecules

A

large molecules (>10,000 Daltons) usually composed of polymers of similar or identical parts (monomers or residues)

44
Q

metabolism

A

entire network of biochemical reactions which occur in living cells

45
Q

methionine

A

an amino acid with a thio ether side chain functional group (Met) [M]

46
Q

motif

A

a unique combination or folding of secondary structures

47
Q

net charge

A

the algebraic sum of all the charges on a single molecule

48
Q

nucleic acid

A

biopolymers consisting of nitrogenous bases which are linked to ribose or deoxyribose linked by phosphodiester bonds

49
Q

P50

A

is the partial pressure of usually oxygen at which the biomolecule is half saturated with oxygen

50
Q

PAGE

A

an acronym for PolyAcrylamide Gel Electrophoresis

51
Q

pH

A

the negative of the logarithm of the hydronium ion concentration = -log [H+]

52
Q

phenylalanine

A

an amino acid with a benzyl or phenyl side chain functional group (Phe) [F]

53
Q

pKa

A

the negative of the logarithm of the acid dissociation constant

54
Q

positive cooperativity

A

cooperativity in which the subsequent events become easier

55
Q

primary structure

A

linear sequence of amino acids in a polypeptide or protein

56
Q

proline

A

an amino acid with a pyrrolidine ring side chain functional group (Pro) [P]

57
Q

protein

A

polymer of alpha amino acids linked by peptide [amide] bond

58
Q

quaternary structure

A

the association of multiple tertiary structures to form a complex

59
Q

residue

A

the monomeric component of a polymer minus the atoms which were removed to make the chemical linkage

60
Q

secondary structure

A

the regular or periodic folding of the primary structure

61
Q

serine

A

an amino acid with a primary aliphatic alcohol side chain functional group (Ser) [S] {pka 16}

62
Q

side chain

A

(R group) the atoms of an amino acid which are attached to the alpha carbon of an amino acid and which are not the carboxyl group, amino group or hydrogen

63
Q

stereoisomers

A

two different configurations of a molecule

64
Q

tertiary structure

A

the irregular or non-repeating folding of the primary and secondary structures

65
Q

threonine

A

an amino acid with a secondary alcohol side chain functional group (Thr) [T] {pka 16}

66
Q

tryptophan

A

an amino acid with an indole side chain functional group (Trp) [W]

67
Q

tyrosine

A

an amino acid with a phenol (aromatic alcohol) side chain functional group (Tyr) [Y] {pka 10.5}

68
Q

valine

A

an amino acid with a branched aliphatic side chain functional group (Val) [V]

69
Q

zwitter ion

A

a molecule which contains both positive and negative charges but is electrically neutral

70
Q

aspartate

A

an amino acid with a carboxylic acid side chain functional group (Asp) [D] {pka 3.9}

Biochemistry (11 decks)

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