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Biochemistry > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

Amino acid

A

Central carbon atom bonded to a carbonyl group, an amino group, a hydrogen and the R Group

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2
Q

Carbohydrates

A

Compounds made up of carbon, hydrogen and oxygen

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3
Q

Nucleotides

A

Unit of the hereditary materials DNA and RNA, composed of a five-carbon sugar, a nitrogen containing ring and one or more phosphate groups

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4
Q

Lipids

A

Poorly soluble in water because they are composed of long chains of hydrocarbons

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5
Q

Monomers

A

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

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6
Q

Polymer

A

Macromolecules formed by the bonding of smaller units

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7
Q

Proteins

A

Macromolecules formed by the polymerization of amino acids

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8
Q

Nucleic acids

A

macromolecules formed by the polymerization of nucleotides

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9
Q

Enzymes

A

Class of proteins that display catalytic activity

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10
Q

Catalytic activity

A

Ability to increase the rate of a chemical reaction

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11
Q

Genetic code

A

Relationship between the nucleotide sequence in nucleic acids and the amino acid sequence in proteins

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12
Q

Thermodynamics

A

Study of transformations and transfer of energy

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13
Q

Covalent bonds

A

Hold atoms together in a molecule, small distance between atoms, shared electrons

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14
Q

non-covalent interactions

A

Weaker, relies on electrostatic and electro negativity forces, not sharing electrons

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15
Q

Non polar covalent bond

A

Equal size atoms where the electrons are shared equally
0.5 or less is non polar

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16
Q

Polar covalent bond

A

Different sizes where electrons are shared unequally
0.5-2 is polar

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17
Q

Electronegativity

A

Measure of the force of an atom’s attraction for electrons it shares in a chemical bond with another atom

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18
Q

Induced dipole-dipole interactions

A

London dispersion force, attraction between two transiently induced dipoles

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19
Q

Dipole interactions

A

Noncovalent associations based on weak attractions of dipoles for one another

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20
Q

Dipole induced dipole interactions

A

Permanent dipole in one molecule can induce a transient dipole in another molecule

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21
Q

Dipole-dipole interactions

A

Forces that occur between molecules that are dipoles, partial positive side of a molecule attracts the partial negative side of another molecule

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22
Q

Ion dipole forces

A

Occurs when ions in solution interact with molecules that have dipoles form hydration shells (ionic bond)

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23
Q

Salt bridge

A

Oppositely charged molecules in close proximity, seen in protein structures

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24
Q

Hydrophilic

A

Water loving

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25
Q

Hydrophobic

A

Water hating

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26
Q

Hydrophobic interactions

A

Attractions between non polar molecules

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27
Q

Amphipathic

A

Molecule that contains both hydrophobic and hydrophilic regions

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28
Q

Michelle formation by amphipathic molecules

A

Spherical arrangement of organic molecules in water are clustered so that their hydrophobic parts are inside and hydrophilic are outside

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29
Q

Hydrogen bonds

A

Always linear, noncovalent attractive interactions when the positive end of one dipole is a hydrogen atom bonded to a highly electronegative atom and the negative end is an atom with a lone pair

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30
Q

How many hydrogen bonds can a water molecule have

A

4 hydrogen bonds

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31
Q

Acid

A

Molecule that behaves as a proton donor, produces H+ in aqueous solution

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32
Q

Base

A

Molecule that behaves as a proton acceptor, produce OH- in aqueous medium

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33
Q

Acid strength

A

Tendency of an acid to dissociate to a hydrogen ion and its conjugate base, characterized by acid dissociation constant

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34
Q

Strong acid

A

Strong electrolyte, almost all acid molecules ionize to H+

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35
Q

Strong base

A

Strong electrolyte where almost all base molecules form OH- ions

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36
Q

Weak acid

A

A weak electrolyte where only a small percentage of molecules ionize to form H+

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37
Q

Weak base

A

A weak electrolyte where only a small percentage of the base molecules form OH- ions

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38
Q

Titration

A

Experiment in which measured amounts of base are added to an acid

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39
Q

Equivalence point

A

Point in an acid-base titration at which enough base has been added to neutralize the acid

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40
Q

Inflection point

A

Point in titration curve where pH=pKa and HA=A

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41
Q

Buffer solutions

A

Tend to resist change in pH when small to moderate amounts of a strong acid or strong base are added

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42
Q

Zwitterions

A

Compounds that have both a positive and negative charge

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43
Q

Amino group

A

NH2 functional group

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44
Q

Carbonyl group

A

COOH functional group that dissociates to give the carboxylate anion

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45
Q

Alpha carbon

A

Bonded to a hydrogen and to the side chain group, R

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46
Q

Side chain group

A

Aka R group, portion of an amino acid that determines its identity

47
Q

Stereoisomers

A

Molecules that differ from each other only in their configuration

48
Q

Chiral compounds

A

Have non-superimposable mirror images

49
Q

Which of the 20 amino acids is not chiral

A

Glycine

50
Q

Nonpolar amino acid definition

A

Group of amino acids that has nonpolar side chains and is hydrophobic

51
Q

What are the nonpolar amino acids?

A

Glycine, alanine,valine, leucine, isoleucine, proline, phenylalanine, tryptophan and methionine

52
Q

These 4 non polar amino acids contain an aliphatic hydrocarbon group

A

Alanine, valine, leucine and isoleucine

53
Q

Which nonpolar amino acid has an aliphatic cyclic structure?

A

Proline

54
Q

Which nonpolar amino acid has an aromatic hydrocarbon group?

A

Phenylalanine

55
Q

Which nonpolar amino acid contains an indole side chain that is aromatic

A

Tryptophan

56
Q

Which nonpolar amino acid obtains a sulfur atom and aliphatic hydrocarbon groupings?

A

Methionine

57
Q

Polar-neutral amino acids definition

A

Group of amino acids that has polar side chains that are electrically neutral at neutral pH

58
Q

What are the polar-neutral amino acids?

A

Serine, theronine, tyrosine, cysteine, glutamine and asparagine

59
Q

Which two polar-neutral amino acids has their polar group as a hydroxyl bonded to aliphatic hydrocarbon groups?

A

Serine and threonine

60
Q

Which polar-neutral amino acid has the hydroxyl group bonded to an aromatic hydrocarbon group?

A

Tyrosine

61
Q

Which polar-neutral amino acid has a polar side chain that contains a thiol group

A

Cysteine

62
Q

Which two polar-neutral amino acids have amide groups in their side chains?

A

Glutamine and asparagine

63
Q

What are the basic amino acids?

A

Histidine lysine and arginine

64
Q

What is the charge of the side chains on a basic amino acid at pH 7

A

Positive

65
Q

In which basic amino acid is the side-chain amino group attached to an aliphatic hydrocarbon chain?

A

Lysine

66
Q

In which basic amino acid is the side chain a guanidino group bonded to an aliphatic hydrocarbon chain?

A

Arginine

67
Q

In which basic amino acid is the side chain an imidazole group?

A

Histidine

68
Q

Uncommon amino acids

A

Derived from common amino acids and produced through posttranslational modification

69
Q

How many ionizable group on monoprotic acids?

A

1 and 1 pKa

70
Q

How many ionizable groups in diprotic acids?

A

2 and 2 pKas

71
Q

How many ionizable groups does polyprotic acids have?

A

3 or more with a pKa for each ionizable group

72
Q

what types of weak acids are the amino acids?

A

Diprotic or triprotic

73
Q

Peptide bond

A

Amide bond between amino acids in a protein

74
Q

Peptides

A

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

75
Q

Polypeptide chain

A

Backbone of a protein formed by linking amino acids by peptide bonds

76
Q

Native conformations

A

3-D shapes of proteins with biological activity

77
Q

Primary structure

A

Order in which amino acids are covalently linked together

78
Q

Secondary structure

A

Ordered 3-D arrangement in space of the backbone atoms in a polypeptide chain

79
Q

Tertiary structure

A

3-D arrangement of all atoms in a protein including those in side chains and prosthetic groups

80
Q

Quaternary structure

A

Arrangement of subunits with respect to one another

81
Q

Backbone hydrogen bonding

A

Between polar side chains of amino acids

82
Q

Disulfide bond

A

Oxidation of the thiol groups of two cysteines to form a covalent bond

83
Q

Denaturation

A

Unraveling of a macromolecule caused by the breakdown of noncovalent interactions

84
Q

Causes of denaturation

A

Heat, large changes in pH, detergents, denaturants and 6-mercaptoethanol

85
Q

Quaternary structure of proteins

A

Pertains to proteins that consist of more than one polypeptide chain

86
Q

Oligomers

A

Molecules that are made up of a number of smaller subunits

87
Q

Allosteric

A

Property of multisubunit proteins such that a conformational change in one subunit includes a drastic change in another subunits

88
Q

Myoglobin

A

Consists of a one polypeptide chain of 153 amino acid residues and a prosthetic group, heme in a hydrophobic pocket

89
Q

Prosthetic group

A

Tightly bound, non polypeptide unit required for biological function of some proteins

90
Q

Positive cooperativity

A

When one O2 is bound, it becomes easier for the next one to bind

91
Q

Phi bond

A

Bond between the alpha carbon and amino nitrogen of that residue

92
Q

Psi bond

A

Between the alpha carbon and carbonyl carbon of that residue

93
Q

Alpha helix

A

H-bonds between carbonyl oxygen of one amino acid and the amino group of an amino acid four residues away

94
Q

Beta sheet

A

H-bonds between different parts of the primary sequence

95
Q

Parallel beta sheet

A

Amino acid sequence runs in the same direction

96
Q

Anti-parallel beta sheet

A

Neighboring strands run in opposite direction

97
Q

How many residues for each turn of the alpha helix?

A

3.6

98
Q

What are the 3 factors that disrupt the alpha helix?

A

Bending of the backbone by proline, strong electrostatic repulsion and steric repulsion

99
Q

Beta bulge

A

Common non repetitive irregular secondary motif in anti parallel beta sheets

100
Q

Reverse turns

A

Parts of the proteins where the polypeptide chain folds back on itself, contains glycine or proline

101
Q

Beta alpha beta unit

A

Two parallel strands of beta sheet are connected by a stretch of alpha helix

102
Q

Alpha alpha unit

A

Contains two anti parallel alpha helix, aka helix turn helix

103
Q

Beta meander

A

Antiparallel sheet is formed by a series of tight reverse turns connecting stretches of polypeptide chain

104
Q

Greek key

A

Formed when a polypeptide chain doubles back on itself

105
Q

Motifs

A

Repetitive supersecondary structures

106
Q

Beta barrel

A

Created when beta sheets are extensive enough to fold back on themselves

107
Q

Collagen triple helix

A

Consists of three polypeptide chains wrapped around each other to form water-insoluble fibers of great strength

108
Q

Globular proteins

A

Poly peptide backbone folds on itself to produce a compact globular shape

109
Q

Bioinformatics

A

Involves searching the databases of known structures for sequence homology

110
Q

Liposomes

A

Spherical aggregates of lipids arranged so that the polar head groups are in contact with water adn the nonpolar tails are away from water

111
Q

Protein-folding chaperones

A

Aid in the correct and timely folding of many proteins

112
Q

Cofactors

A

Functional non-amino acid component that are metal ions or organic molecules

113
Q

coenzymes

A

Organic cofactors such as NAD+ in lactate dehydrogenase

Biochemistry (3 decks)

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