Exam 1 Flashcards
(141 cards)
1
Q
Two classes of proteins unique to enamel
A
amelogenins and enamelins
2
Q
What cells secrete dentin?
A
odontoblasts
3
Q
What makes up the dentin organic matrix?
A
fibrous collagens (90%) and proteins (10%)
ex) proteoglycans, phosphoproteins, and phospholipids
4
Q
6 most common elements in biological molecules
A
Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorous, and Sulfur
5
Q
What isomers of sugars do humans use?
A
D-sugars
6
Q
What isomers of amino acids do humans use?
A
L-amino acids
7
Q
What are the 3 most abundant macromolecules?
A
Proteins, nucleic acids, and polysaccharides
8
Q
Average size of prokaryotic cells
A
1-2 micrometers
9
Q
Average size of Eukaryotic cells
A
10-100 micrometers
10
Q
What is the average weight of an amino acid?
A
113 daltons
11
Q
What percentage of a cells weight is made up by proteins?
A
20%
12
Q
What process allows for more possible proteins to be formed than the number of genes that code for them?
A
Alternative RNA splicing
13
Q
Hydrophobic amino acids
A
Alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, tryptophan
14
Q
Hydrophilic amino acids
A
Lysine, arginine, histidine, aspartate, glutamate, serine, threonine, asparagine, glutamine
15
Q
Special amino acids
A
Cysteine, glycine, proline
16
Q
Which amino acid has two nitrogens and can bind to metals?
A
Histidine
17
Q
Which amino acid is very rigid and is responsible for kinking?
A
Proline
18
Q
Which amino acid is the most flexible and can fit into small places?
A
Glycine
19
Q
Which amino acid(s) can be phosphorylated?
A
Serine, threonine, and tyrosine
20
Q
Which amino acid(s) can be glycosylated?
A
Asparagine, serine, and threonine
21
Q
Which amino acids can be hydroxylated?
A
Proline and lysine
22
Q
What functional groups are present in monosaccharides?
A
A hydroxyl group and either an aldehyde or a ketone
23
Q
What is the most common storage carbohydrate in animal cells?
A
Glycogen
24
Q
List the dissociation constant (Kd) concentrations for:
1) High affinity
2) Moderate affinity
3) Weak affinity
A
1) 10^-9 M
2) 10^-6 M
3) 10^-3 M
25
pH inside of a cell
7.2
26
pH inside lysosomes
4.5
27
What type of reaction is described by a negative Gibb's free energy?
exergonic
28
What type of reaction is described by a positive Gibb's free energy?
endergonic
29
Enthalpy
A measure of the energy of a system
30
Entropy
A measure of disorder in a system
31
Is the Enthalpy of a exothermic reaction positive or negative?
negative
32
Is the Enthalpy of a endothermic reaction positive or negative?
positive
33
How much energy is released by the cleavage of the phosphodiester bond?
-7.3 kcal/mol
34
What is the function of structural proteins?
To help determine a cells shape
35
What is the function of scaffold proteins?
To assemble proteins to perform functions
36
What is the function of enzymes?
Catalyze chemical reactions
37
What is the function of membrane transport proteins?
Transportation of ions and molecules across membranes
38
What is the function of regulatory proteins?
To act as a signal, sensors, and switches to control processes
39
What is the function of signaling proteins?
To transmit extracellular signals to the cell's interior
40
What is the function of motor proteins?
movement
41
Genome
A complete set of genes for an organism
42
Proteome
A complete set of proteins for an organism
43
Approximately how many genes are in the human genome?
25,000
44
Approximately how many proteins can be encoded by the genes in the human genome?
33,000
45
What type of structure is function derived from?
3-D structure
46
What type of interactions form three-dimensional structure?
noncovalent interactions
47
What comprises the primary structure of proteins?
Amino acid chains (polypeptides)
48
What are the three common types of secondary structures?
alpha-helix
beta-sheet
beta-turn
49
What forms the tertiary structure?
Overall folding of secondary structures bonded together by disulfide bonds
50
Three categories of tertiary structure
Fibrous, globular, and integral membrane proteins
51
What is the less common type of secondary structure that can be formed?
Random coil
52
What is a macromolecular machine?
The transcription-initiation complex
53
What are three important other structural motifs?
Coiled-coil, EF hand, and Zinc finger
54
What comprises the Coiled-coil structural motif?
Leucine zipper made of -Leu-Val-Leu-Asn-
55
What comprises the EF hand structural motif?
alpha-helix, beta-turn (loop), alpha-helix
56
What comprises the zinc finger structural motif?
alpha-helix and beta-turn
57
```
All of the following can disrupt protein folding except:
A) heat
B) pH fluctuations
C) urea
D) high concentration saline solution
E) guanidine hydrochloride
F) beta-mercaptoethonal
```
D
58
Protein folding is promoted by what?
Chaperones (proteins)
59
What are Chaperonins?
folding champers
60
What causes Alzheimer's disease?
A buildup of beta-amyloid plaques in the brain
61
What is a ligand?
A molecule to which a protein binds to
62
What are two properties that dictate how a protein binds to its ligand?
specificity & affinity
63
Binding specificity
Ability of a protein to bind to one molecule in preference to another
64
Binding affinity
The strength of binding
65
Epitope
Binding site in the protein
66
What is an enzymes ligand?
Their substrate
67
What comprises the Active site?
The substrate binding site and the catalytic site
68
What is the Michaelis constant (Km)?
A measure of the affinity of an enzyme for its substrate
69
How can you find Km for an enzyme-catalyzed reaction?
Km = 1/2 Vmax
70
What are the three types of active binding sites in serine proteases?
Trypsin, Chymotrypsin, and Elastase
71
Proteosome
A complex molecular machine used to degrade proteins
72
What controls protein life-span?
Regulated protein degradation
73
What is Ubiquitin and what does it do?
Ubiquitin is a 76 amino acid long peptide that marks cytosolic proteins for degradation by proteasomes.
74
Covalent modifications of peptides
hydrolysis or addition of a molecule to a side-chain, N-, or C-terminus
75
Noncovalent modifications allows for what?
cooperative regulation of proteins
76
What does proteolytic cleavage do?
Irreversibly activates or inactivates some proteins
77
In a GTPase switch, when GTP is bound, is the switch active or inactive?
Active
78
What is GEF & what does it do?
GEF is the GTPase activator protein which phosphorylates GDP to GTP so that the GTP can bind to the GTPase and activate the switch
79
Protein kinase action in phosphorylation & dephosphorylation
dephosphorylates ATP to ADP and binds the phosphate group to the target protein to activate the switch
80
Protein phosphatase action in phosphorylation & dephosphorylation
Removes the phosphate group from the target protein and phosphorylates ADP to ATP to deactivate the switch
81
Centrifugation techniques separate proteins by what?
Mass and density
82
SDS-PAGE separates proteins based on what?
Mass
83
Two dimensional gel electrophoresis separates proteins by what?
Charge and mass
84
How does gel-filtration chromatography separate proteins?
Size (large vs. small)
85
How does ion-exchange chromatography separate proteins?
Positive vs. negative charge
86
Western blotting (immunoblotting)
Combination of techniques to resolve and detect proteins
87
Three techniques that are combined to perform a western blot
1) Electrophoresis & transfer
2) Antibody detection
3) Chromogenic detection
88
Pulse-chase experiments
Tracks the pathway of protein modifications or movement within cells
89
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry
Determines molecular mass by using a laser to accelerate ions towards a detector.
90
Electrospray ionization ion-trap mass spectrometrys
determine the molecular mass of proteins and peptides
91
X-ray crystallography
Provides diffraction data to determine the 3-D structure of a protein
92
LC-MS/MS
Used to identify the proteins in a complex biological sample
93
What two techniques can be used to identify many of the proteins in organelles?
Density-gradient centrifugation and LC-MS/MS
94
Proteomics
Study of all or a large subset of proteins in a biological system
95
What binds to the zinc in the zinc finger motif?
Histidine and Cysteine
96
What binds to the calcium in the EF hand motif?
Glutamate, Aspartate, Asparagine, and Threonine
97
Nascent protein
Native or unfolded protein
98
What type of bonds hold antibodies & antigens together?
Noncovalent
99
What type of bonds hold proteins together?
Covalent
100
What type of bonds hold nucleic acids together?
Covalent
101
What type of bonds hold polysaccharides together?
Covalent
102
What type of bonds hold most macromolecules together?
Noncovalent
103
What are the three main enzymes that are involved in ubiquitination?
Ubiquitin-activating enzyme (E1), Ubiquitin-conjugating enzyme (E2), Ubiquitin ligase (E3)
104
What are two types of centrifugation?
Differential and Rate-zonal centrifugation
105
What does SDS do?
Attaches to the protein to give it a negative charge
106
Three types of chromatography
Gel-filtration, antibody-affinity, and ion-exchange chromatography
107
What is ultimately responsible for governing cellular functions?
Nucleic acids
108
Type of bonds that connect nucleic acid monomers
phophodiester bonds
109
DNA is made of a double helix of what type of strands?
complementary and anti-parallel
110
What type of helix is the majority of DNA?
right-handed helix beta DNA
111
How is alpha DNA formed?
When the water is removed form beta DNA
112
What is zDNA?
Short DNA molecules composed of alternating purine-pyrimidine nucleotides that adopt a left-handed helix
113
Why can DNA bend and condense?
There are no hydrogen bonds parallel to the axis
114
What is chromatin?
Condensed DNA-protein complex in eukaryotic cells
115
What is the unwinding and separation of the DNA strands known as?
denaturation or melting
116
What enzyme relieves torsional strain on DNA?
Topoisomerase
117
What enzyme combines the separated strands of DNA back together?
Ligase
118
template DNA is transcribed into a complementary RNA chain by 1)______ to generate RNA in the 2)____ direction.
1) RNA polymerase
| 2) 5' to 3'
119
In the elongation step of transcription, which direction does RNA polymerase advance?
3' to 5'
120
What is an operon?
A contiguous array of genes that encode proteins which function together
121
Exons
coding sequences
122
Introns
non-protein coding sequences
123
Types of mRNA processing
5' cap, poly A tail addition, RNA splicing, and Alternative RNA splicing
124
What does mRNA provide during translation?
codons
125
What does tRNA provide during translation?
anticodons
126
What does rRNA do during translation?
Form ribosomes that catalyze the assembly of amino acids into a protein
127
What is responsible for non-standard base pairing?
Third base position wobble
128
What characteristic describes the three letter genetic code?
The code is degenerate
129
What two things does translation require?
tRNA and aminoacyl-tRNA synthetases
130
What type of bases does tRNA contain?
Modified bases
131
What is Inosine?
Deaminated adenine
132
What are ribosomes?
protein-synthesizing machines
133
What are ribosomes made of?
Complexes of rRNA and proteins
134
What are the three domains of a ribosome?
A site, P site, E site
135
What recognizes the AUG start codon?
Methionyl-tRNA
136
What facilitates the recognition of the initiating AUG sequence?
A sequence of surrounding nucleotides known as the Kozak sequence
137
DNA replication follows what type of mechanism?
Semiconservative
138
What direction does DNA replication proceed?
5' to 3'
139
What enzyme unwinds during DNA replication?
DNA helicase
140
What is required for DNA replication?
An RNA or DNA primer
141
What are the 3 stop codons?
UAG, UAA, and UGA
