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Flashcards in Molecular Biology Deck (149):
1

What type of RNAs code for proteins?

mRNA

2

What type of RNA forms the basic structure of the ribosome and catalyzes protein synthesis?

rRNA (ribosomal)

3

What type of RNA is central to protein synthesis as an adaptor between mRNA and amino acid?

tRNA (transfer)

4

What type of RNA functions in a variety of nuclear processes, including the splicing of pre-mRNA?

snRNA (small nuclear)

5

What type of RNA helps to process and chemical modify rRNAs?

snoRNA (Small nucleolar)

6

What type of RNA regulates gene expression by blocking translation of specific mRNAs and causes their degradation?

miRNA (micro)

7

What type of RNA turns off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structures?

siRNA (small interfering)

8

Prokaryotic transcription requires recruitment of _______ factor to the RNA polymerase. In order for transcription to continue and elongation to occur, this factor must be released.

Sigma

9

Initiation of eukaryotic transcription begins with the binding of _______ to the ______ box

TFIID
TATA

[the subunit of TFIID that recognizes TATA is called TATA-box-binding protein or TBP]

10

During initiation of eukaryotic transcription, once TFIID has bound the TATA box, what is the next factor to be recruited? This is followed by what other factors?

TFIIB, followed by TFIIF, RNA polymerase II, TFIIE, and TFIIH

11

Which of the initiation factors in eukaryotic transcription serves to unwind the DNA double helix and expose the DNA template strand?

TFIIH

12

During initiation of eukaryotic transcription, phosphorylation of _______ by TFIIH causes the polymerase to leave the promoter and begin elongation

CTD

13

In short, the most important factor for initiation in prokaryotic transcription is _______, while in eukaryotic transcription it is the ______ factors.

Sigma
TFII

14

What 3 methods of processing must RNA go through in eukaryotics prior to translation?

RNA capping at 5' end (with 7-methyl guanosine)

RNA splicing (intron removal)

Polyadenylation at 3' end (addition of poly A tail)

15

Each group of 3 consecutive nucleotides in RNA is called a codon. Each codon specifies either one amino acid or a stop in the translation process. A total of ____ triplet codons code for the _____ known amino acids, thus the code is _____________

61
20
Degenerate

16

What is the start codon of the genetic code?

Met = AUG

17

What are the 3 possible stop codons in the genetic code?

UAA
UAG
UGA

18

The ____________ hypothesis postulates that the genetic code is read by molecules that can recognize a codon and carry the corresponding amino acid.

Adaptor

19

What serves as an adaptor that binds to a specific codon and brings with it an amino acid for incorporation into the polypeptide chain?

tRNA

20

tRNA has a ____________ secondary structure with 4 short double-helical segments. Two regions of unpaired nucleotides are crucial to the functions of tRNA: the _____________ loop, which is a set of 3 consecutive nucleotides that pair with a complementary codon in an mRNA molecule, and the ________ __________ region which binds the amino acid that matches the corresponding codon.

Cloverleaf
Anticodon
3' CCA terminal

21

The genetic code is translated by 2 adaptors: how does the correct tRNA with the correct amino acid come to the mRNA?

Aminoacyl tRNA synthetase has a binding site for both amino acid and codon

22

During translation, what enzyme catalyzes the translocation of 2 complete subunits to the A site?

Peptidyl transferase

23

What are the 3 ribosomal sites E, P, and A for during translation?

A = incoming tRNA with new amino acid

P = for polypeptide chain

E = exit

24

During elongation, two things are occuring simultaneously, one is the growth of the amino acid chain, what is the other?

Proofreading, as incorrectly base-paired tRNAs preferentially dissociate

25

What is unique about stop codons?

They are not recognized by any tRNA and do not code for any amino acid

26

What type of protein recognizes stop codons and what do they do?

Release Factors (RFs), which promote release of completed proteins from tRNAs by binding to the A site of the ribosome containing the stop codon and catalyzing the addition of water instead of an amino acid

27

What are the 3 general types of protein transport?

Gated transport
Transmembrane transport
Vesicular transport

28

Protein transfer/transport to various compartments is guided by ________ _________, which are streches of amino acids usually 15-60 residues long and are localized to N or C terminus or within the protein sequence.

Sorting signals

29

Multiple, scattered sequences of sorting signals brought together by protein folding are known as a what?

Signal patch

30

Signal sequences are both necessary and sufficient for protein targeting. They are recognized by _____________ receptors.

Complementary

31

What removes the sorting signal after a protein reaches its final destination?

Signal peptidase

32

What type of transport is nuclear transport?

Gated transport, bidirectional and selective

33

What are the sorting signals called that direct molecules to the nucleus and where are they found?

Nuclear localization signals (NLS), located at many different sites on protein (can be N terminus, C terminus, or within protein sequence)

34

Nuclear localization signals are recognized by nuclear import receptors (NIRs) or nuclear export receptors (NERs). Which of the following is also an important shuttle for a protein with an NLS?

A. Ran
B. Rab
C. Ras
D. Rho

A. Ran

Ran-GDP and Ran-GTP are utilized in nuclear import and export [note that the GTP form is always within the nucleus]

35

Describe the directionality of transmembrane transport such as mitochondrial transport

Unidirectional

36

Most mitochondrial proteins are encoded in ________ DNA

Nuclear

37

Signal sequences on mitochondrial proteins are located where? - these direct proteins to the correct compartment in mitochondria and specific receptor proteins recognize their configuration. Multi-subunit protein complexes called protein translocators mediate translocation

They are located towards the ends of the proteins to make ampiphilic nuclear structures

38

What type of mitochondrial membrane translocator transports all nuclear encoded proteins in the outer membrane?

TOM

39

What type of mitochondrial membrane translocator inserts beta barrel proteins in the outer membrane?

SAM

40

What type of mitochondrial membrane translocator mediates the insertion of proteins in the inner membrane and matrix?

TIM23

41

What type of mitochondrial membrane translocator mediates the insertion of transporters in the inner membrane?

TIM22

42

What type of mitochondrial membrane translocator mediates the insertion of mitochondrially synthesized proteins?

OXA

43

Transport across the endoplasmic reticulum requires an ER signal sequence guided to the ER membrane by what 2 components?

SRP = signal recognition particle, and an SRP receptor

44

The SRP utilized in transport across the ER is rod-shaped with a large ___________ pocket lined by methionines.

Hydrophobic


This pocket can accommodate hydrophobic signal sequences of different sizes, shapes, and sequences

45

What is the role of the ER signal sequence and SRP in directing ribosomes to the ER membrane?

The SRP has the hydrophobic pocket that recognizes proteins supposed to go to the ER. The SRP hugs the ribosome, holds translation (stopping protein synthesis), and brings the entire unit to the ER membrane with another translocator which allows it through the ER membrane and into the lumen

46

Proteins and other biomolecules are transported via transport vesicles, which bud off from primary compartments and fuse with the next one. They come in different shapes and sizes. The contents of the vesicle are called ________ and transport is __________

Cargo
Directional

47

There are 3 different vesicular transport systems, what are they?

Biosynthetic - for newly synthesized proteins

Endocytic - proteins coming from outside thru PM into the cell

Retrieval - taking proteins back to previous compartment to maintain homeostasis

48

The budding off of cargo into a vesicle involves the formation of what at the plasma membrane?

Clathrin coat

49

The specificity in vesicle targeting is achieved by surface markers on vesicles and complementary receptors on the target membrane. _______ proteins direct vesicles to specific spots on the target membrane, while ________ proteins mediate fusion of the vesicles with the membrane

Rab
SNARE

50

The sorting of lysosomal proteins requires ________, which is the signal for the protein destined to go to the lysosome

M6P


[recall that this signal must be uncovered by addition of p-GlcNAc]

51

It can be challenging to isolate a single protein from thousands of others present in a cell. _________ DNA technology can be used to overexpress a protein prior to purification. This allows purification of ________ proteins. A _________________ ______________ typically needs to be done to reduce the complexity of the material prior to purification

Recombinant
Endogenous
Sub-cellular fractionation

52

During sub-cellular fractionation, a suspension of different cell types is subjected to centrifugation, which separates different cell types based on _______ and ________

Size
Density

53

What type of centrifugation allows for the separation of organelles?

Ultracentrifugation

54

What laboratory technique allows for the purification of a single protein from individual organelles?

Column chromatography

55

There are 3 different matrices for column chromatography, what are they?

Ion-exchange chromatography - separates based on charge

Gel-filtration chromatography - separates based on size

Affinity chromatography - based on specific ligand

56

What laboratory technique takes a mixture of proteins, applies uniform negative charge, and thus allows you to separate the proteins based on SIZE?

SDS-PAGE

57

Once you run SDS-PAGE to separate your proteins based on size, what laboratory method would you use to identify a specific protein?

Mass spectrometry

58

What is the primary use of mass spectrometry?

Identification of unknown proteins

59

What laboratory technique allows you to analyze specific, known proteins to learn more about them?

Western blotting

60

What laboratory technique allows you to detect and quantify proteins based on color change and works by utilizing antibodies?

ELISA - can be direct or indirect

61

Where are the instructions for producing a multicellular animal contained?

Non-coding regulatory DNA, which contains regulatory elements that serve as binding sites for gene regulatory proteins

62

Cells that are fated to develop into a specialized cell type despite changes in the environment are called ___________

Determined

63

Cells that can change rapidly due to alterations in environment are called ____________

Completely undetermined

64

Cells that have some attributes of a particular cell type but can change with environment are called __________

Committed

65

What is characteristic of phase 1 of neural development?

Division and differentiation into different cell types (neurons, glia, muscle cells); and cells are not connected

66

What is characteristic of phase 2 of neural development?

Axons and dendrites grow out along specific routes setting up a provisional but orderly network of connections

67

What is characteristic of phase 3 of neural development?

Continues into adult life, connections are adjusted and refined through interactions with distant regions via electric signals

68

During the migration of neurons, the tip of the axon/dendrite has an irregular, spiky enlargement called the what?

Growth cone, these crawl through surrounding tissue, trailing the axon or dendrite behind


One of the growth cones starts migrating fast and develops axon-specific proteins which will form the axon

69

Growth cone behavior is dictated by cytoskeletal machinery. They throw out __________ and __________

Filopodia and lamelopodia

70

What are the 2 monomeric GTPases that control assembly/disassembly of actin filaments, which control the movement of the growth cones?

Rho and Rac

71

What are the 2 major cues exploited by growth cones to find their way?

Extracellular matrix environment (sensed by receptors present on the membrane)

Chemotactic factors (released by neighboring cells) - provide contact guidance

72

Chemotactic factors are secreted by cells and act as guidance factors at strategic points along the path. These may be attractive or repulsive. Which of the following is/are attractive chemotactic factors?

A. Netrin
B. Slit
C. Semaphorin
D. B and C

A. Netrin

73

Chemotactic factors are secreted by cells and act as guidance factors at strategic points along the path. These may be attractive or repulsive. Which of the following is/are repulsive chemotactic factors?

A. Netrin
B. Slit
C. Semaphorin
D. B and C

D. B and C

74

The guidance of ___________ neurons involves movement from the roof of the developing neural plate toward Netrin in the floor attracting processes from top to bottom. An abrupt switch in direction occurs in response to Slit and Semaphorin released at that point

Commissural

75

What are released from target cells for incoming cells to tell them to synapse?

Neurotrophic factors

Cells that do not get enough of these will die off

76

"Neurons that fire together, wire together" represents what neuronal process that is based upon the functional connectivity of neurons?

Synaptic remodelling

77

Which layer of skin creates a water barrier?

Epidermis

78

Which layer of skin is the fatty subcutaneous layer?

Hypodermis

79

What layer of skin is rich in collagen and provides toughness?

Dermis

80

Name the 4 layers of the epidermis from top to bottom (from keratinized squame to the CT of the dermis)

Squame (keratinized)
Granular cell layer
Prickle cell layer
Basal cell layer
Basal lamina
Connective tissue of dermis

81

Stem cells are not terminally differentiated, can _________ without limit, and undergo ________ division

Divide
Slow

82

What are the 2 theories as to how stem cells give rise to one stem cell and one cell with potential to differentiate?

Asymmetric division
Independent choice

83

What type of cells are formed from stem cells but divide very quickly and have a finite number of divisions, and at the end they do differentiate into a desired cell type?

Transit amplifying cells

84

How often is your olfactory epithelium replaced?

Every 30 days

85

Describe olfactory neurons

Bipolar, with dendrite facing EC environment and an axon that travels along the olfactory nerve to the olfactory bulb in the brain

86

Where are the stem cells associated with the olfactory system located?

In the basal lamina

87

Olfactory neurons connect all the way to the brain, where they synapse at _________

Glomeruli

88

The free surfaces of cilia at the end of olfactory neurons have odorant receptor proteins. What type of receptors are these?

G protein coupled receptors

89

An activated olfactory receptor in turn activates an intracellular ______ protein, which activates __________ ___________ which produces cyclic AMP. The opening of ion channels in the PM results in an influx of ________ and __________ into the cell, causing an AP

G
Adenylate cyclase
Sodium; calcium

90

If a cell is able to produce its own growth factor and does not require outside input, what type of signaling does it utilize?

A. Endocrine
B. Paracrine
C. Autocrine
D. Juxtacrine

C. Autocrine

91

What are the 3 main types of cell signaling receptors in the PM?

Ion-channels
GPCRs
RTKs (enzyme-coupled)

92

Signaling that occurs via intracellular mechanism releasing cAMP which activates PKA involves what type of receptor?

A. GPCR
B. RTK
C. Ion-channel linked receptor
D. None of the above

A. GPCR

93

Which of the following types of receptors includes Ras signaling to downstream MAP kinases?

A. GPCR
B. RTK
C. Ion-channel linked
D. None of the above

B. RTK

94

If you see "downstream of phosphorylation event" what type of receptor is it?

RTK

95

What are the major accessory proteins to actin?

ARPs

96

What proteins are microtubules associated with for regulation of stability?

Tau

97

What is the major type of intermediate filament discussed in class?

Keratin

98

Differentiate between cadherins and integrins

Integrins connect to the basal lamina (cell matrix)

Cadherins connect cells to each other

99

________________ consist of a long polysaccharide/core complex linked to an extensive hyaluronic acid chain and are examples of lactose digestion from dietary sources

Proteoglycans

100

What is the structure of collagen?

Triple helix

101

Which of the following is involved in a hydroxylation event involving a triple helix of repeating peptide sequences?

A. Proteoglycan
B. Collagen
C. Cadherin
D. None of the above

B. Collagen

102

Mitochondria are ___________ when they are associated with the microtubular cytoskeleton. They are more _________ when they are associated with muscle fibers in high energy cells.

Dynamic; fixed

103

What is the identifying feature of transit amplifying cells according to Theisen?

Limited number of divisions

104

Where are embryonic stem cells harvested from?

The inner cell mass

105

DNA is a double helix with overall _____ charge due to phosphate backbone. It is complementary and antiparallel. The free end is the ____ end and the end with the OH group is ______

Negative
5'
3'

106

What type of DNA repair would be utilized in the case of a deaminated C?

Base excision repair, which uses a glycosylase to check strands by flipping bases out

107

What type of DNA repair would be utilized in the case of a pyrimidine dimer?

Nucleotide excision repair

108

Nonhomologous end joining and homologous recombination are important in the repair of double stranded breaks. During what times in the cell cycle is each used, and which is more accurate?

Nonhomologous end joining can occur at any time in the cell cycle, but is not very high fidelity

Homologous recombination occurs during S and G2 phase and is the most accurate

109

When does crossing over occur?

Prophase I of meiosis I

110

Sequence specific transcription factors are modular. What are the 4 types of modules?

DNA-binding module
Dimerization module
Activation module
Regulatory module

111

Which of the following is the simplest DNA binding motif with a longer helix portion for DNA recognition; these proteins bind DNA as dimers.

A. Leucine zipper
B. Zinc finger motif
C. Helix-loop-helix
D. Helix-turn-helix

D. Helix-turn-helix

112

Which of the following includes a zinc atom and binds to the major groove of DNA?

A. Leucine zipper
B. Zinc finger motif
C. Helix-loop-helix
D. Helix-turn-helix

B. Zinc finger motif

113

Which of the following contains two alpha-helical DNA binding domains and contains interactions between hydrophobic amino acid side chains at every 7-amino acids down the side of the alpha helix?

A. Leucine zipper
B. Zinc finger motif
C. Helix-loop-helix
D. Helix-turn-helix

A. Leucine zipper

114

Which of the following can occur as homodimers or heterodimers and contains 3 domains: DNA binding domain, dimerization domain, and activation domain?

A. Leucine zipper
B. Zinc finger motif
C. Helix-loop-helix
D. Helix-turn-helix

C. Helix-loop-helix

115

What dictates the stability of RNA?

The poly-A tail!

116

___________ is an apparatus that deliberately destroys aberrant proteins, thus regulating protein degradation

Proteasome

117

Prader willie is an example of what type of control of gene expression?

Genomic imprinting

118

What are the 3 checkpoints to the cell cycle control system?

CP 1: start (chromosome duplication)

CP 2: G2/M (metaphase)

CP 3: metaphase to anaphase transition

119

Cdks are the heart of the cell cycle control system. Describe the levels vs. activity of Cdks.

Cdks levels remain constant, their activity rises and falls

Cyclin levels are what vary depending on time in the cell cycle

120

What is required for full activation of cyclin-Cdks?

Phosphorylation of Cdk at the T loop (cave site) by CAK

121

How do Wee1 and Cdc25 control Cdk-cyclin activities?

Wee1 kinase adds inhibitory phosphate to Cdk-cyclin complex roof site, Cdc25 removes it

122

P27 is a protein that can bind to the Cdk-cyclin complex and make the entire thing inactive, it is known for targeting G1/S Cdk and S-Cdks. What type of controller is this?

CKI (Cdk inhibitory protein)

123

If sister chromatids were pulled apart at the end of S phase, there would be breaks. To avoid this, cells reorganize sister chromatids into short structures that can be pulled apart at anaphase with no breakage. What is the two step process for this, and what brings it about?

Condensation
Resolution

Brought about by condensin

124

What activates APC/C to complete mitosis?

M-Cdk

125

Once M-Cdk activates APC/C to complete mitosis, Cdc20 is added to make APC/C fully active. Separase enzyme is freed from ________ by ubiquitination so that it can cleave and dissociate __________

Securin
Cohesins

126

Which of the following involves depolymerization of the plus end of the microtubule which drives the pulling of the kinetochore poleward?

A. Depolymerization
B. Microtubule flux
C. Polar ejection force

A

127

Which of the following results in a push-pull phenomenon?

A. Depolymerization
B. Microtubule flux
C. Polar ejection force

C. Polar ejection force

128

Which of the following involves microtubules being moved toward spindle poles with tubulin added at plus ends while being dismantled at minus ends?

A. Depolymerization
B. Microtubule flux
C. Polar ejection force

B. Microtubule flux

129

In utero, you have webbing between your fingers which is removed by a form of programmed cell death called ________

Apoptosis

130

Caspases are synthesized first as an inactive precursor called procaspases. What are the 2 types of active caspases?

Initiator caspases
Executioner caspases

131

Describe the intrinsic pathway of apoptosis

When CYTOCHROME C is released from the mitochondria, it binds to a protein called APAF1 which forms the APOPTOSOME

132

________ proteins become activated, form aggregation in mitochondrial outer membrane, and induce the release of cytochrome c so that the apoptosome can form

BH123

133

_______ proteins regulate intrinsic apoptosis by inhibiting BH123 from aggregating in the mitochondrial membrane

Bcl2

134

Are Bcl2 proteins oncogenes or tumor suppressor genes?

Oncogenes

135

What does BH3 protein do to control apoptosis?

BH3 prevents activation of Bcl2 so that BH123 is free to form the pore

136

What type of protein blocks caspases, thus preventing initiation of apoptosis?

IAPs, these may be neutralized by anti-IAPs so apoptosis can occur

137

What terms are associated with oncogenes?

Overactivity mutation

Gain of function

Dominant

"Gas pedal"

138

What terms are associated with tumor suppressor genes?

Underactivity mutation

Loss of function

Recessive

Brake pedal

139

Which of the following is characterized by a hyperactive protein made in normal amounts?

A. Deletion or point mutation in coding sequence
B. Regulatory mutation
C. Gene amplification
D. Chromosomal rearrangement

A

140

Which of the following is characterized by a normal protein greatly overproduced?

A. Deletion or point mutation in coding sequence
B. Regulatory mutation
C. Gene amplification
D. Chromosomal rearrangement

B and C

141

Which of the following is characterized by nearby regulatory DNA sequences causing normal proteins to be overproduced, or fusion to actively transcribed gene produces a hyperactive fusion protein?

A. Deletion or point mutation in coding sequence
B. Regulatory mutation
C. Gene amplification
D. Chromosomal rearrangement

D.

142

What are the 2 major categories of tumor suppressor genes?

Proteins that normally restrict cell growth and proliferation

Proteins that maintain integrity of the genome

143

What are the 2 types of retinoblastoma?

Hereditary (40%, both eyes affected)

Sporadic (60%, single tumor in one eye)

144

Which form of Rb is associated with a loss of heterozygosity?

Hereditary form, bc one good copy gets eliminated and tumor forms

145

What hypothesis characterizes the sporadic form of Rb?

Two hit hypothesis, 2 normal Rb genes so one is hit, then the second (more rare bc of this)

146

What is the term for the precursor to colorectal cancer?

Polyp (aka adenoma)

147

Is APC an oncogene or tumor suppressor gene?

Tumor suppressor

148

Is K-ras an oncogene or tumor suppressor gene?

Oncogene (40% of colorectal cancers have point mutation in Kras)

149

Is p53 an oncogene or tumor suppressor gene?

Mother of all tumor suppressor genes, 60% of colorectal cancers have inactivating mutation of p53