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DENT-D512 Molecular Cell Biology > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

Two classes of proteins unique to enamel

A

amelogenins and enamelins

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2
Q

What cells secrete dentin?

A

odontoblasts

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3
Q

What makes up the dentin organic matrix?

A

fibrous collagens (90%) and proteins (10%)

ex) proteoglycans, phosphoproteins, and phospholipids

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4
Q

6 most common elements in biological molecules

A

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorous, and Sulfur

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5
Q

What isomers of sugars do humans use?

A

D-sugars

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6
Q

What isomers of amino acids do humans use?

A

L-amino acids

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7
Q

What are the 3 most abundant macromolecules?

A

Proteins, nucleic acids, and polysaccharides

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8
Q

Average size of prokaryotic cells

A

1-2 micrometers

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9
Q

Average size of Eukaryotic cells

A

10-100 micrometers

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10
Q

What is the average weight of an amino acid?

A

113 daltons

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11
Q

What percentage of a cells weight is made up by proteins?

A

20%

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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

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13
Q

Hydrophobic amino acids

A

Alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, tryptophan

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14
Q

Hydrophilic amino acids

A

Lysine, arginine, histidine, aspartate, glutamate, serine, threonine, asparagine, glutamine

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15
Q

Special amino acids

A

Cysteine, glycine, proline

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16
Q

Which amino acid has two nitrogens and can bind to metals?

A

Histidine

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17
Q

Which amino acid is very rigid and is responsible for kinking?

A

Proline

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18
Q

Which amino acid is the most flexible and can fit into small places?

A

Glycine

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19
Q

Which amino acid(s) can be phosphorylated?

A

Serine, threonine, and tyrosine

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20
Q

Which amino acid(s) can be glycosylated?

A

Asparagine, serine, and threonine

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21
Q

Which amino acids can be hydroxylated?

A

Proline and lysine

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22
Q

What functional groups are present in monosaccharides?

A

A hydroxyl group and either an aldehyde or a ketone

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23
Q

What is the most common storage carbohydrate in animal cells?

A

Glycogen

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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

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25
Q

pH inside of a cell

A

7.2

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26
Q

pH inside lysosomes

A

4.5

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27
Q

What type of reaction is described by a negative Gibb’s free energy?

A

exergonic

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28
Q

What type of reaction is described by a positive Gibb’s free energy?

A

endergonic

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29
Q

Enthalpy

A

A measure of the energy of a system

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30
Q

Entropy

A

A measure of disorder in a system

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31
Q

Is the Enthalpy of a exothermic reaction positive or negative?

A

negative

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32
Q

Is the Enthalpy of a endothermic reaction positive or negative?

A

positive

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33
Q

How much energy is released by the cleavage of the phosphodiester bond?

A

-7.3 kcal/mol

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34
Q

What is the function of structural proteins?

A

To help determine a cells shape

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35
Q

What is the function of scaffold proteins?

A

To assemble proteins to perform functions

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36
Q

What is the function of enzymes?

A

Catalyze chemical reactions

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37
Q

What is the function of membrane transport proteins?

A

Transportation of ions and molecules across membranes

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38
Q

What is the function of regulatory proteins?

A

To act as a signal, sensors, and switches to control processes

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39
Q

What is the function of signaling proteins?

A

To transmit extracellular signals to the cell’s interior

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40
Q

What is the function of motor proteins?

A

movement

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41
Q

Genome

A

A complete set of genes for an organism

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42
Q

Proteome

A

A complete set of proteins for an organism

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43
Q

Approximately how many genes are in the human genome?

A

25,000

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44
Q

Approximately how many proteins can be encoded by the genes in the human genome?

A

33,000

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45
Q

What type of structure is function derived from?

A

3-D structure

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46
Q

What type of interactions form three-dimensional structure?

A

noncovalent interactions

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47
Q

What comprises the primary structure of proteins?

A

Amino acid chains (polypeptides)

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48
Q

What are the three common types of secondary structures?

A

alpha-helix
beta-sheet
beta-turn

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49
Q

What forms the tertiary structure?

A

Overall folding of secondary structures bonded together by disulfide bonds

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50
Q

Three categories of tertiary structure

A

Fibrous, globular, and integral membrane proteins

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51
Q

What is the less common type of secondary structure that can be formed?

A

Random coil

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52
Q

What is a macromolecular machine?

A

The transcription-initiation complex

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53
Q

What are three important other structural motifs?

A

Coiled-coil, EF hand, and Zinc finger

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54
Q

What comprises the Coiled-coil structural motif?

A

Leucine zipper made of -Leu-Val-Leu-Asn-

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55
Q

What comprises the EF hand structural motif?

A

alpha-helix, beta-turn (loop), alpha-helix

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56
Q

What comprises the zinc finger structural motif?

A

alpha-helix and beta-turn

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57
Q 
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
A

D

58
Q

Protein folding is promoted by what?

A

Chaperones (proteins)

59
Q

What are Chaperonins?

A

folding champers

60
Q

What causes Alzheimer’s disease?

A

A buildup of beta-amyloid plaques in the brain

61
Q

What is a ligand?

A

A molecule to which a protein binds to

62
Q

What are two properties that dictate how a protein binds to its ligand?

A

specificity & affinity

63
Q

Binding specificity

A

Ability of a protein to bind to one molecule in preference to another

64
Q

Binding affinity

A

The strength of binding

65
Q

Epitope

A

Binding site in the protein

66
Q

What is an enzymes ligand?

A

Their substrate

67
Q

What comprises the Active site?

A

The substrate binding site and the catalytic site

68
Q

What is the Michaelis constant (Km)?

A

A measure of the affinity of an enzyme for its substrate

69
Q

How can you find Km for an enzyme-catalyzed reaction?

A

Km = 1/2 Vmax

70
Q

What are the three types of active binding sites in serine proteases?

A

Trypsin, Chymotrypsin, and Elastase

71
Q

Proteosome

A

A complex molecular machine used to degrade proteins

72
Q

What controls protein life-span?

A

Regulated protein degradation

73
Q

What is Ubiquitin and what does it do?

A

Ubiquitin is a 76 amino acid long peptide that marks cytosolic proteins for degradation by proteasomes.

74
Q

Covalent modifications of peptides

A

hydrolysis or addition of a molecule to a side-chain, N-, or C-terminus

75
Q

Noncovalent modifications allows for what?

A

cooperative regulation of proteins

76
Q

What does proteolytic cleavage do?

A

Irreversibly activates or inactivates some proteins

77
Q

In a GTPase switch, when GTP is bound, is the switch active or inactive?

A

Active

78
Q

What is GEF & what does it do?

A

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
Q

Protein kinase action in phosphorylation & dephosphorylation

A

dephosphorylates ATP to ADP and binds the phosphate group to the target protein to activate the switch

80
Q

Protein phosphatase action in phosphorylation & dephosphorylation

A

Removes the phosphate group from the target protein and phosphorylates ADP to ATP to deactivate the switch

81
Q

Centrifugation techniques separate proteins by what?

A

Mass and density

82
Q

SDS-PAGE separates proteins based on what?

A

Mass

83
Q

Two dimensional gel electrophoresis separates proteins by what?

A

Charge and mass

84
Q

How does gel-filtration chromatography separate proteins?

A

Size (large vs. small)

85
Q

How does ion-exchange chromatography separate proteins?

A

Positive vs. negative charge

86
Q

Western blotting (immunoblotting)

A

Combination of techniques to resolve and detect proteins

87
Q

Three techniques that are combined to perform a western blot

A

1) Electrophoresis & transfer
2) Antibody detection
3) Chromogenic detection

88
Q

Pulse-chase experiments

A

Tracks the pathway of protein modifications or movement within cells

89
Q

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry

A

Determines molecular mass by using a laser to accelerate ions towards a detector.

90
Q

Electrospray ionization ion-trap mass spectrometrys

A

determine the molecular mass of proteins and peptides

91
Q

X-ray crystallography

A

Provides diffraction data to determine the 3-D structure of a protein

92
Q

LC-MS/MS

A

Used to identify the proteins in a complex biological sample

93
Q

What two techniques can be used to identify many of the proteins in organelles?

A

Density-gradient centrifugation and LC-MS/MS

94
Q

Proteomics

A

Study of all or a large subset of proteins in a biological system

95
Q

What binds to the zinc in the zinc finger motif?

A

Histidine and Cysteine

96
Q

What binds to the calcium in the EF hand motif?

A

Glutamate, Aspartate, Asparagine, and Threonine

97
Q

Nascent protein

A

Native or unfolded protein

98
Q

What type of bonds hold antibodies & antigens together?

A

Noncovalent

99
Q

What type of bonds hold proteins together?

A

Covalent

100
Q

What type of bonds hold nucleic acids together?

A

Covalent

101
Q

What type of bonds hold polysaccharides together?

A

Covalent

102
Q

What type of bonds hold most macromolecules together?

A

Noncovalent

103
Q

What are the three main enzymes that are involved in ubiquitination?

A

Ubiquitin-activating enzyme (E1), Ubiquitin-conjugating enzyme (E2), Ubiquitin ligase (E3)

104
Q

What are two types of centrifugation?

A

Differential and Rate-zonal centrifugation

105
Q

What does SDS do?

A

Attaches to the protein to give it a negative charge

106
Q

Three types of chromatography

A

Gel-filtration, antibody-affinity, and ion-exchange chromatography

107
Q

What is ultimately responsible for governing cellular functions?

A

Nucleic acids

108
Q

Type of bonds that connect nucleic acid monomers

A

phophodiester bonds

109
Q

DNA is made of a double helix of what type of strands?

A

complementary and anti-parallel

110
Q

What type of helix is the majority of DNA?

A

right-handed helix beta DNA

111
Q

How is alpha DNA formed?

A

When the water is removed form beta DNA

112
Q

What is zDNA?

A

Short DNA molecules composed of alternating purine-pyrimidine nucleotides that adopt a left-handed helix

113
Q

Why can DNA bend and condense?

A

There are no hydrogen bonds parallel to the axis

114
Q

What is chromatin?

A

Condensed DNA-protein complex in eukaryotic cells

115
Q

What is the unwinding and separation of the DNA strands known as?

A

denaturation or melting

116
Q

What enzyme relieves torsional strain on DNA?

A

Topoisomerase

117
Q

What enzyme combines the separated strands of DNA back together?

A

Ligase

118
Q

template DNA is transcribed into a complementary RNA chain by 1)______ to generate RNA in the 2)____ direction.

A

1) RNA polymerase

2) 5’ to 3’

119
Q

In the elongation step of transcription, which direction does RNA polymerase advance?

A

3’ to 5’

120
Q

What is an operon?

A

A contiguous array of genes that encode proteins which function together

121
Q

Exons

A

coding sequences

122
Q

Introns

A

non-protein coding sequences

123
Q

Types of mRNA processing

A

5’ cap, poly A tail addition, RNA splicing, and Alternative RNA splicing

124
Q

What does mRNA provide during translation?

A

codons

125
Q

What does tRNA provide during translation?

A

anticodons

126
Q

What does rRNA do during translation?

A

Form ribosomes that catalyze the assembly of amino acids into a protein

127
Q

What is responsible for non-standard base pairing?

A

Third base position wobble

128
Q

What characteristic describes the three letter genetic code?

A

The code is degenerate

129
Q

What two things does translation require?

A

tRNA and aminoacyl-tRNA synthetases

130
Q

What type of bases does tRNA contain?

A

Modified bases

131
Q

What is Inosine?

A

Deaminated adenine

132
Q

What are ribosomes?

A

protein-synthesizing machines

133
Q

What are ribosomes made of?

A

Complexes of rRNA and proteins

134
Q

What are the three domains of a ribosome?

A

A site, P site, E site

135
Q

What recognizes the AUG start codon?

A

Methionyl-tRNA

136
Q

What facilitates the recognition of the initiating AUG sequence?

A

A sequence of surrounding nucleotides known as the Kozak sequence

137
Q

DNA replication follows what type of mechanism?

A

Semiconservative

138
Q

What direction does DNA replication proceed?

A

5’ to 3’

139
Q

What enzyme unwinds during DNA replication?

A

DNA helicase

140
Q

What is required for DNA replication?

A

An RNA or DNA primer

141
Q

What are the 3 stop codons?

A

UAG, UAA, and UGA

DENT-D512 Molecular Cell Biology (1 decks)

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