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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
Hydrophobic
Water hating
26
Hydrophobic interactions
Attractions between non polar molecules
27
Amphipathic
Molecule that contains both hydrophobic and hydrophilic regions
28
Michelle formation by amphipathic molecules
Spherical arrangement of organic molecules in water are clustered so that their hydrophobic parts are inside and hydrophilic are outside
29
Hydrogen bonds
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
30
How many hydrogen bonds can a water molecule have
4 hydrogen bonds
31
Acid
Molecule that behaves as a proton donor, produces H+ in aqueous solution
32
Base
Molecule that behaves as a proton acceptor, produce OH- in aqueous medium
33
Acid strength
Tendency of an acid to dissociate to a hydrogen ion and its conjugate base, characterized by acid dissociation constant
34
Strong acid
Strong electrolyte, almost all acid molecules ionize to H+
35
Strong base
Strong electrolyte where almost all base molecules form OH- ions
36
Weak acid
A weak electrolyte where only a small percentage of molecules ionize to form H+
37
Weak base
A weak electrolyte where only a small percentage of the base molecules form OH- ions
38
Titration
Experiment in which measured amounts of base are added to an acid
39
Equivalence point
Point in an acid-base titration at which enough base has been added to neutralize the acid
40
Inflection point
Point in titration curve where pH=pKa and HA=A
41
Buffer solutions
Tend to resist change in pH when small to moderate amounts of a strong acid or strong base are added
42
Zwitterions
Compounds that have both a positive and negative charge
43
Amino group
NH2 functional group
44
Carbonyl group
COOH functional group that dissociates to give the carboxylate anion
45
Alpha carbon
Bonded to a hydrogen and to the side chain group, R
46
Side chain group
Aka R group, portion of an amino acid that determines its identity
47
Stereoisomers
Molecules that differ from each other only in their configuration
48
Chiral compounds
Have non-superimposable mirror images
49
Which of the 20 amino acids is not chiral
Glycine
50
Nonpolar amino acid definition
Group of amino acids that has nonpolar side chains and is hydrophobic
51
What are the nonpolar amino acids?
Glycine, alanine,valine, leucine, isoleucine, proline, phenylalanine, tryptophan and methionine
52
These 4 non polar amino acids contain an aliphatic hydrocarbon group
Alanine, valine, leucine and isoleucine
53
Which nonpolar amino acid has an aliphatic cyclic structure?
Proline
54
Which nonpolar amino acid has an aromatic hydrocarbon group?
Phenylalanine
55
Which nonpolar amino acid contains an indole side chain that is aromatic
Tryptophan
56
Which nonpolar amino acid obtains a sulfur atom and aliphatic hydrocarbon groupings?
Methionine
57
Polar-neutral amino acids definition
Group of amino acids that has polar side chains that are electrically neutral at neutral pH
58
What are the polar-neutral amino acids?
Serine, theronine, tyrosine, cysteine, glutamine and asparagine
59
Which two polar-neutral amino acids has their polar group as a hydroxyl bonded to aliphatic hydrocarbon groups?
Serine and threonine
60
Which polar-neutral amino acid has the hydroxyl group bonded to an aromatic hydrocarbon group?
Tyrosine
61
Which polar-neutral amino acid has a polar side chain that contains a thiol group
Cysteine
62
Which two polar-neutral amino acids have amide groups in their side chains?
Glutamine and asparagine
63
What are the basic amino acids?
Histidine lysine and arginine
64
What is the charge of the side chains on a basic amino acid at pH 7
Positive
65
In which basic amino acid is the side-chain amino group attached to an aliphatic hydrocarbon chain?
Lysine
66
In which basic amino acid is the side chain a guanidino group bonded to an aliphatic hydrocarbon chain?
Arginine
67
In which basic amino acid is the side chain an imidazole group?
Histidine
68
Uncommon amino acids
Derived from common amino acids and produced through posttranslational modification
69
How many ionizable group on monoprotic acids?
1 and 1 pKa
70
How many ionizable groups in diprotic acids?
2 and 2 pKas
71
How many ionizable groups does polyprotic acids have?
3 or more with a pKa for each ionizable group
72
what types of weak acids are the amino acids?
Diprotic or triprotic
73
Peptide bond
Amide bond between amino acids in a protein
74
Peptides
Molecules formed by linking two to several dozen amino acids by amide bonds
75
Polypeptide chain
Backbone of a protein formed by linking amino acids by peptide bonds
76
Native conformations
3-D shapes of proteins with biological activity
77
Primary structure
Order in which amino acids are covalently linked together
78
Secondary structure
Ordered 3-D arrangement in space of the backbone atoms in a polypeptide chain
79
Tertiary structure
3-D arrangement of all atoms in a protein including those in side chains and prosthetic groups
80
Quaternary structure
Arrangement of subunits with respect to one another
81
Backbone hydrogen bonding
Between polar side chains of amino acids
82
Disulfide bond
Oxidation of the thiol groups of two cysteines to form a covalent bond
83
Denaturation
Unraveling of a macromolecule caused by the breakdown of noncovalent interactions
84
Causes of denaturation
Heat, large changes in pH, detergents, denaturants and 6-mercaptoethanol
85
Quaternary structure of proteins
Pertains to proteins that consist of more than one polypeptide chain
86
Oligomers
Molecules that are made up of a number of smaller subunits
87
Allosteric
Property of multisubunit proteins such that a conformational change in one subunit includes a drastic change in another subunits
88
Myoglobin
Consists of a one polypeptide chain of 153 amino acid residues and a prosthetic group, heme in a hydrophobic pocket
89
Prosthetic group
Tightly bound, non polypeptide unit required for biological function of some proteins
90
Positive cooperativity
When one O2 is bound, it becomes easier for the next one to bind
91
Phi bond
Bond between the alpha carbon and amino nitrogen of that residue
92
Psi bond
Between the alpha carbon and carbonyl carbon of that residue
93
Alpha helix
H-bonds between carbonyl oxygen of one amino acid and the amino group of an amino acid four residues away
94
Beta sheet
H-bonds between different parts of the primary sequence
95
Parallel beta sheet
Amino acid sequence runs in the same direction
96
Anti-parallel beta sheet
Neighboring strands run in opposite direction
97
How many residues for each turn of the alpha helix?
3.6
98
What are the 3 factors that disrupt the alpha helix?
Bending of the backbone by proline, strong electrostatic repulsion and steric repulsion
99
Beta bulge
Common non repetitive irregular secondary motif in anti parallel beta sheets
100
Reverse turns
Parts of the proteins where the polypeptide chain folds back on itself, contains glycine or proline
101
Beta alpha beta unit
Two parallel strands of beta sheet are connected by a stretch of alpha helix
102
Alpha alpha unit
Contains two anti parallel alpha helix, aka helix turn helix
103
Beta meander
Antiparallel sheet is formed by a series of tight reverse turns connecting stretches of polypeptide chain
104
Greek key
Formed when a polypeptide chain doubles back on itself
105
Motifs
Repetitive supersecondary structures
106
Beta barrel
Created when beta sheets are extensive enough to fold back on themselves
107
Collagen triple helix
Consists of three polypeptide chains wrapped around each other to form water-insoluble fibers of great strength
108
Globular proteins
Poly peptide backbone folds on itself to produce a compact globular shape
109
Bioinformatics
Involves searching the databases of known structures for sequence homology
110
Liposomes
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
Protein-folding chaperones
Aid in the correct and timely folding of many proteins
112
Cofactors
Functional non-amino acid component that are metal ions or organic molecules
113
coenzymes
Organic cofactors such as NAD+ in lactate dehydrogenase

Biochemistry (3 decks)

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