1
Q
What are the three noncovalent biological bonds? List them from strongest to weakest.
A
Ionic Bonds
Hydrogen Bonds
Van Der Waals Interactions
2
Q
Occurs between anions and cations.
A
Ionic Bond
3
Q
Occurs when two electronegative atoms share a hydrogen. They share the electron density from the hydrogen atom.
A
Hydrogen Bond
4
Q
Dipoles created by the movement of electron clouds around an atom.
A
Van Der Waals Interactions
5
Q
Surrounds cations and anions due to the nature of water.
A
Hydration Layer
6
Q
Molecules with a ___________________ dissolve in water due to the dipole-dipole interactions.
A
Dipole Moment
7
Q
Molecules that readily interact with water are ______.
A
Hydrophilic
8
Q
_________ molecules do not readily interact with water because they don’t have permanent ________.
A
Hydophobic
Dipoles
9
Q
In a biological solution, hydrophobic molecules will associate together due to what?
A
Formulation of a network of hydrogen bonds between the solvent and water molecules.
10
Q
What are the building blocks of protein?
A
Amino Acids
11
Q
What are the building blocks of glycosaminoglycans?
A
Polymers of alternating amino sugars and sugar acids
12
Q
What are the building blocks of DNA?
A
Deoxyribonucleic acids
13
Q
What are the building blocks of RNA?
A
Ribonucleic acids
14
Q
Completely dissociate (charged) when placed in water.
A
Strong Electrolytes
15
Q
Maintain an equilibrium between charged/uncharged (dissolved/undissolved) when placed in water.
A
Weak Electrolytes
16
Q
___= -log [H+]
A
pH
17
Q
__=[H+][A-]/[HA]
A
Ka
18
Q
__ = -log[Ka]
A
pKa
19
Q
The charged (+ or -) from a molecule is found in under specific conditions.
A
Ionization state
20
Q
pH = pKa + log [conjugate base]/[conjugate acid] or [unprotonated]/[protonated] or [A-]/[HA]
A
Henderson-Hasselbalch equation
21
Q
______ are resistant to change in pH.
A
Buffers
22
Q
The amount of acid acid or base that can be added before a significant change in pH occurs.
A
Buffer capacity
23
Q
In the horizontal area of a titration curve the _______ is resistant to change.
A
pH
24
Q
Where pH = pKa on a titration curve.
A
Inflection point
25
The point on a titration curve where a molecule has completely changed states.
Midway point
26
Tris (short for tris-(hydroymethyl)aminomehtane) is a commonly used buffer for biochemical solutions. It contains an ionizable amino group with pKa = 8.1. What is the ratio of charged to uncharged Tris at physiological pH?
5:1
27
C1 on a carbohydrate is the __________
anomeric
28
When the hydroxyl group is up it is the __ anomer.
Beta
29
When the hydroxyl group is down it is the __ anomer.
Alpha
30
A free aldehyde on a sugar that is able to react.
Reducing sugar
31
Conversion of a sugar in water between the two anomeric forms and open chain form of a sugar.
Mutarotation
32
The joining of a few sugars.
Oligosaccharides
33
The bond between a sugar and another sugar or base in a nucleotide.
Glycosidic Bond
34
The bond between a sugar and another sugar or base in a nucleotide.
Glycosidic Bond
35
Long polymers of repeating disaccharides. The individual sugars are modified by sulfates and the C6 group is often a carboxylate rather than an alcohol.
Glycosaminoglycans
36
16:0
Palmitate
37
Is palmitate saturated or unsaturated?
Saturated
38
18:0
Stearate
39
Is stearate saturated or unsaturated?
Saturated
40
18:1delta9
Oleate
41
Is oleate saturated or unsaturated
Monounsaturated
42
18:2delta9,12
Linoleate
43
What class is Linoleate?
omega 6 fatty acid
44
18:3delta9,12,15
Linolenate
45
What class is linolenate?
omega 3 fatty acid
46
20:4delta5,8,11,14
Arachidonate
47
What class is arachidonate?
omega 6 fatty acid
48
22:6delta4,7,10,13,16,19
Docosahexaenoate (DHA)
49
What class is docosahexaenoate?
omega 3 fatty acid
50
Fatty acids esterified to the three hydroxyls on a glycerol bachbone. They are neutral and so hydrophobic they coalesce together to form droplets.
Triglycerides
51
Any number of lipids that contain a phosphate in the molecule. They are amphipathic molecules that are the basis for lipid bilayers.
Phopholipids
52
Consist of 2 fatty acid linkages to the C1 and C2 carbons of the glycerol backbone.
Glycerophospholipids
53
Consist of 2 fatty acid linkages to the C1 and C2 carbons of the glycerol backbone.
Glycerophospholipids
54
Hydrocarbon chains with a terminal carboxylate group.
Fatty Acids
55
Hydrocarbon chains that contain one C-C double bond.
Monounsaturated
56
Hydrocarbon chains containing more than one C-C double bond.
Polyunsaturated
57
The first carbon of a fatty acid following the carboxylate group is named __. The second carbon is named __. The last carbon is named __.
Alpha
Beta
Omega
58
The longer the carbon chain length, the _____ the melting temperature.
Higher
59
Saturated carbon chains have a ______ melting point than unsaturated carbon chains.
Higher
60
Saturated fatty acids are _________ at room temperature.
Solid
61
Unsaturated fatty acids are ______ at room temperature.
Liquid
62
These lipids form in such a way that their hydrophobic sections associate with each other and their hydrophilic sections associate with surrounding water.
Amphipathic
63
A single layer of amphipathic lipids with the hydrophilic head groups pointing outwards and the hydrophobic tails pointing inwards.
Micelles
64
Form a spherical bilayer with an aqueous compartment at the core.
Vesicles
65
Implies that biological membranes are not uniform distributions and are in motion.
Fluid Mosaic Model
66
Lack of symmetry, one side of the membrane does not look like the other side.
Asymmetry
67
Diffusion across the plane of the membrane.
Lateral Diffusion
68
Diffusion across the membrane itself
Transverse Diffusion
69
When a fatty acid chain is longer than the melting point is ________ and the membrane is ______ fluid.
Higher
| Less
70
The more saturated a fatty acid chain is the ________ the melting point and the membrane is _______ fluid.
Higher
| Less
71
Proteins that attached to the surface of the membrane. They are easily removed by ionic strength solutions. They are not present in the lipid portion of the bilayer.
Peripheral membrane proteins
72
Proteins that are embedded in the lipid bilayer and can only be removed by actions that disrupt the membrane.
Integral membrane proteins
73
What characteristics must molecules have to be able to diffuse across the lipid membrane and enter cells by simple diffusion?
Lipid-soluble, small, and uncharged
74
True or False? The primary driving force that stabilizes lipid bilayers is the formation of hydrophobic bonds between fatty acid chains phospholipids.
False
75
What will increase the fluidity of biological membranes?
Increase the percentage of unsaturated fatty acids in the phospholipids.
76
What describes the major structural difference between phophatidylcholine (PC) and sphingomyelin (SM)?
SM is hydrophobic; PC is amphipathic.
77
Palmitic acid has a pKa of ~4.5. What fraction of palmitic acid is charged under normal physiologial conditions?
~1000 charged for each uncharged
78
```
All of the following are unsaturated fatty acids except?
A. stearate
B. oleate
C. linoleic acid
D. arachidonate
```
A. Stearate
79
```
All of the following lipids have a glycerol backbone except?
A. plasmalogen
B. Ceramide
C. Triglyceride
D. lecithin
```
B. Ceramide: has a serine backbone
80
Cholesterol has ____ carbons and ____ rings.
27
| 4
81
All glycolipids are derivatives of __________.
Palmitate and Serine
82
```
Which of the lipids would not be present in biological membranes?
A. Plasmalogen
B. Ceramide
C. Triglyceride
D. Lecithin
```
C. Triglyceride
83
```
Membrane fluidity is affected by all of the following except?
A. phospholipid fatty acid chain length
B. membrane protein composition
C. cholesterol content
D. saturation of fatty acids
```
B. membrane protein composition
84
Rank the following molecules on the basis of membrane permeability, from highest to lowest.
- Leucine
- Heparin
- Glucose
- Palmitic acid
- Oxygen
- Oxygen
- Leucine
- Palmitic Acid
- Glucose
- Heparin
85
Specific groups of atoms responsible for reaction behaivor.
Functional Groups
86
Atoms included in the amino acid that are not part of the backbone.
Side Chains
87
The charge that is present on different parts of an amino acid depending on the pka and pH.
Ionic Form
88
Amino acid containing both a positive and negative charge.
Zwitterion
89
What is Leucine classified as?
Aliphatic (non ring containing)
90
What is Isoleucine classified as?
Aliphatic (non ring containing)
91
What is Alanine classified as?
Aliphatic (non ring containing)
92
What is Proline classified as?
Aliphatic (non ring containing)
93
What is Valine classified as?
Aliphatic (non ring containing)
94
What is Valine classified as?
Aliphatic (non ring containing)
95
What is Phenylalanine classified as?
Aromatic (ring containing)
96
What is Tyrosine classified as?
Aromatic (ring containing)
97
What is Tryptophan classified as?
Aromatic (ring containing)
98
What is Cysteine classified as?
Sulfur-containing
99
What is Methionine classified as?
Sulfur-containing
100
What is Serine classified as?
Aliphatic Hydroxyl
101
What is Threonine classified as?
Aliphatic Hydroxyl
102
What is Arginine classified as?
Basic
103
What is Histidine classified as?
Basic and Imidazole
104
What is Lysine classified as?
Basic
105
What is Aspartate classified as?
Acidic
106
What is Glutamate classified as?
Acidic
107
What is Glutamine classified as?
Amide Derivative
108
What is Asparagine classified as?
Amide Derivative
109
What is Tryptophan classified as?
Indole
110
What is Arginine classified as?
Guanidinium
111
Methyl groups added to the N in certain Lysine and Histidine side chains.
Methylation
112
Lysine side chains modified by acetyl groups.
Acetylation
113
Side chains of Asparagine, Serine, and Threonine modified by the addition of oligosaccharides.
Glycosylation
114
Phosphate added to Tyrosine, Serine, and Threonine side chains by an ester bond.
Phosphorylation
115
Modification of Glutamate side chains that creates two carboxylates on the side chain which functions in binding Ca++
Gamma-Carboxylation
116
Proline and Lysine side chains in collagen are hydroxylated that allows collagen to adopt it 3-D shape.
Hydroxylation
117
What is the pKa of Tyrosine?
10.5
118
What is the pKa of Arginine?
12.5
119
What is the pKa of Histidine?
6.0
120
What is the pKa of Lysine?
10.5
121
What is the pKa of Aspartate?
4.0
122
What is the pKa of Glutamate?
4.0
123
What is the predominant ionization state of the imidazole side chain of Histidine at physiological pH?
Cationic
124
What is the net charge of glutamate at physiological pH?
A. -1
B. 0
C. +1
A. -1
125
What is the net charge of glutamate at physiological pH?
A. -1
B. 0
C. +1
A. -1
126
```
Which of the following amino acids would confer hydrophobic porperties on a protein?
A. Glycine
B. Serine
C. Leucine
D. Cysteine
```
A. Glycine
| C. Leucine
127
```
Which of the following amino acids would contribute to protein stability by forming H bond through its side chain?
A. Asparagine
B. Phenylalanine
C. Methionine
D. Isoleucine
```
A. Asparigine
128
Name the two sulfur-containing amino acids.
Cysteine and Methionine
129
Combination of a carboxylate group of one amino acid to the amino group of another amino acid to made an amide.
Peptide Bond
130
The open amino group of a polypeptide.
N-terminal
131
The open carboxylate group end of a polypeptide.
C-terminal
132
Everything but the side chains of a polypeptide.
Backbone
133
Covalent bond linkages between two sulfurs of two different amino acid side chains.
Disulfide Bond
134
True or Flase? The C=O, C-N, and N-H bonds are all in the same plane in a polypeptide?
True
135
True or False? Their is rotation about the C-N bond in a polypeptide?
False
136
The sequence of amino acids that make up a protein.
Primary structure
137
The sequence of amino acids that make up a protein.
Primary structure
138
Locally structured sections within a protein such as alpha helices and beta sheets.
Secondary structure
139
The association of multiple secondary structures within a protein.
Supersecondary structure
140
The final 3-D structure of a protein.
Tertiary structure
141
The association of multiple tertiary structures.
Quaternary structure
142
When a protein is no longer in it's normal 3-D structure.
Denaturation
143
A conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.
Domain
144
A conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.
Domain
145
Typically right handed and is stabilized by hydrogen bonds that occur between a carbonyl oxygen and an amide hydrogen located four residues later in the sequence.
Alpha Helices
146
Backbones spread into an extended strand instead of spiraling. The carbonyl oxygens form hydrogen bonds with the hydrogen from amide groups adjacent structures.
Beta pleated sheets
147
Backbones spread into an extended strand instead of spiraling. The carbonyl oxygens form hydrogen bonds with the hydrogen from amide groups adjacent structures.
Beta pleated sheets
148
Amino acids found on the surface of the protein and help keep the protein soluble.
Hydrophilic amino acids
149
Amino acids that avoid water so they interact with each other to form the interior of the protein.
Hydrophobic amino acids
150
The primary sequence of a protein ultimately determines the final structure.
Anfinsen's Law
151
_______ rich in glycine and proline amino acids, with nearly one-third of the amino acids being glycine. Each _________ molecule adapts a unique left handed helix of about three amino acids per turn. _________ structure is completed by wrapping three ________ subunits around one another in a right handed fashion.
Collagen
152
_______ of protein domains brings substrates close enough so they can react.
Induced-fit
153
Which of the following is the best statement regarding a peptide bond?
A. A peptide bond is a type of weak chemical interaction
B. When a dipeptide is converted to two amino acids, a molecule of water is used
C. During translation, the peptide bond is synthesized cis
D. Because it is a secondary amino acid, proline does not form peptide bonds
B. When a dipeptide is converted to two amino acids, a molecule of water is used
154
True or False? Large changes in the structure of a protein will affect the function of protein?
True
155
Define "primary structure of a protein"
The sequence of amino acids without any folding
156
The structure of an immunoglobulin domain is characterized by?
Beta sandwich
157
Which of the following is a characteristic of the peptide bond?
The N atom shows a pKa 9.5 (check)
158
What tools are used for the measurement of proteins?
Spectrophotometry
Spectrometry
Chromatography
Electrophoresis
159
True or False? Lower mass molecules centrifuge to the bottom faster.
False
160
True or False? More spherically shaped molecules centrifuge to the bottom faster.
True
161
True or False? Higher density molecules centrifuge to the bottom faster.
True
162
Tells how fast a particle sediments in a centrifugal field.
S - Sediment Coefficient
| S is for Svedburg units
163
Using some sort of technique to break open a cell and release its contents so that specifics within can be measured.
Subcellular Fractionation
164
In this technique the solid phase consists of porous beads. The beads have small pores in which the smaller molecules may enter, but the larger ones are excluded. A buffer solution is continuously added and a proteins molecule that cannot fit into the pores will flow down the column in the bulk solution state and elute. Thus separating molecules according to size.
Gel Filtration Chromatography
165
In this technique the solid phase consists of porous beads. The beads have small pores in which the smaller molecules may enter, but the larger ones are excluded. A buffer solution is continuously added and a proteins molecule that cannot fit into the pores will flow down the column in the bulk solution state and elute. Thus separating molecules according to size.
Gel Filtration Chromatography
166
In this technique the solid phase consists of an inert matrix (cellulose or agarose) to which a specific biochemical agent has been covalently coupled. The biochemical agent is a molecule with which the protein of interest specifically interacts. A mixture of protein is applied to the matrix and the specific protein binds. Most of the proteins don't bind and are washed away by buffer. The specific protein can then be eluted off the column by adding a solution containing the same compound that is attached to the matrix. The protein binds the compound in solution and is washed away. Thus, the separation is based on the functional properties of the protein.
Affinity Chromatography
167
The separation is dependent on the surface charge of the protein
Ion Exchange Chromatography
168
Because proteins are charged molecules, they will migrate in an electrical field. The speed at which the molecule will migrate depends on the charge of the molecule and its size (molecular weight).
Electrophoresis
169
How would you determine the pI of a protein?
Use a gel with a pH gradient across it
170
In the Watson-Crick structure of DNA, the H bond forming atoms of the bases are exposed in the major or minor groove?
Major
171
```
All of the following factors determine how a particle sediments in a centifugal field except?
A. mass
B. density
C. charge
D. shape
```
C. Charge
172
What does a nucleotide consist of?
A sugar, a nitrogenous base, and one to three phosphates.
173
How does DNA differ from RNA?
DNA does not contain an OH group on the C2 carbon
174
What's the difference between a nucleotide and a nucleoside?
A nucleoside does not contain any phosphate groups. It's just the sugar and base
175
Anti-parallel stands are known as the __ form.
B
176
When 4 G's associate together in a G rich sequence
G quartet
177
The temperature at which the strands of DNA separate from one another.
Melting temperature
178
What is the equation from melting temperature?
Tm=81*C + 16.6log [Na+] + 0.41(%GC)
179
Why does the melting temperature relate to the watson-crick model?
In the Watson-Crick model of DNA G and C pair together and the melting temperature depends on the percentage of GC bonds
180
What are the differences between DNA and RNA?
- DNA lack the 2' hydroxyl group. DNA contains deoxyribose, RNA contains ribose
- DNA is more stable and can form paired complementary strands
- RNA does not form a double helix and stays single stranded.
Biochemistry
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