Midterm 1 Flashcards
1
Q
when regarding transport of lipids a _______ density means highest in proteins while ________ dense means highest in lipids
A
high, low
2
Q
*would life be possible with a pure lipid bilayer?
A
No
3
Q
simple diffusion rate of substance movement across the phospholipid part of a membrane is proportional to its ______, ________, and _______?
A
concentration gradient
hydrophobicity
size
4
Q
what does a high K value mean when regarding hydrophobicity?
A
greater fraction found in oil, more hydrophobic and faster to cross bilayer
5
Q
what are the 3 groups of membrane transport proteins?
A
Channels, transporters (uniporter, symporter, antiporter), atp powered pumps
6
Q
non gated channels are always ______?
A
open
7
Q
when are gated channels open?
A
open only in response to chemical or electrical signals
8
Q
uiporters transport ____ molecule down its concentration gradient?
A
one
9
Q
symporters and antiporters transport _____ molecules?
A
two
10
Q
secondary active transport includes?
A
symporters and antiporters
11
Q
primary active transport includes?
A
atp powered pumps
12
Q
facilitated transport includes?
A
channels and uniporters (movement down [ ] gradient)
13
Q
why are conformational changes essential for transport proteins?
A
cycles of change expose binding sites to one side of the membrane while another conformational change exposes the other side
14
Q
Na/K pump pumps Na _____ the cell and K _____ the cell.
A
Na out, K in
15
Q
Na/ lysine sympoter brings ______ in the cell along with ___ Na
A
lysine, 2 Na
16
Q
K channel releases K _____ the gradient
A
down
17
Q
what is the modern cell theory?
A
all living things ar emad eup of one or more cells
all cells arise from pre existing cells by division
the cell is the fundamental unit of structure and function in all living organisms
18
Q
what are some common features of cells?
A
contain hereditary information
plasma membranes
energy molecules atp
small molecules
19
Q
cells have ___ forms of amino acids and ____ forms of sugars
A
L amino acids
D sugars
20
Q
what are two characteristics of prokaryotes?
A
no internal membrane compartments
no organelles
bacteria and archaea
generally smaller genomes
21
Q
is eukaryota a monophyletic group?
A
yes
22
Q
what is a main challenge for eukaryotes?
A
moving molecules between internal membrane compartments
23
Q
transcription and translation are coupled in prokaryotes
to or f
A
fasle, they are not
24
Q
processing occurs only in eukaryotes (t or f)
A
true
25
nuclear export occurs in both prokaryotes and eukaryotes
| ( t or f)
false, only eukaryotes
26
what are the four phases of the eukaryotic cell cycle?
```
G1 (gap phase)
S ( synthesis)
G2 ( gap 2)
M (mitosis)
G0 (out of cycle)
```
27
do mitochondria and chloroplasts replecate separately from nuclear dna?
yes
28
what is apicomplexa?
phylum of parasitic alveolates (protists)
29
what are 3 characteristics of apicomplexa?
unicellular, spore forming, complex life cycle, obligate endoparasites, unique organelle (apicoplast)
30
plasmodium is responsible for which disease?
malaria
31
what is the general target of antibiotics?
target bacterial or fungal process
32
what blocks the tunnel in the ribosome that the peptide exists from?
macrolides
33
plastids are an uncommon organelle ( t or f)
true
34
what are 3 common features of model organisms?
small, easy feeding, non dangerous, cheap, simple care, readily availible, short generation time, genome sequenced
35
can bacteria be model organisms?
yes but lack organelled of eukaryotes so there are limitations
36
what are the 3 common model bacterial organims?
ecoli, b subtilis caulobacter crescentus, pseudomonas fluorescens
37
why is yeast studied in classical genetics?
isolate and characterize mutants that lack the ability to do something that normal organism can do
38
mutations can occur randomly or be induced with a chemical or physical _______
mutagen
39
plant cells are interconnected by?
plasmodesmata
40
animal cells are interconnected by?
cell adhesion molecules, matrix called basal lamnia
41
what is collagen made up of?
polysacchides and proteins
42
the function of epithelium is ?
separates external environment, barrier and protective surface
43
only about ____ % of human dna encode proteins while the rest plays a regulatory role
10%
44
why are c elegans a good model organism?
small, short generation of 3 days, transparent, hermaphroditic, simple body plan, model human disease
45
these transgenic worms (c elegans) are commonly used for the expression of what?
GFP , green fluorescence protein
46
what is syteny?
occurence of genes in the same order on a chromosome in two or more different species
47
regulatory proteins include ______ factors
transcription
48
how do proteosomes differ from deutereosomes?
proteosomes (mouth near blastopore and ventral nerve cord)
deutereosomes ( anus near blastopore and dorsal ventral nervous system
49
patterning genes do what?
encode master transcription factors that control other genes and specify the body axes and body segments of an animal
50
monogenic is?
mutation in single gene encoding a single protein
51
the most common hereditary muscle wasting disease is?
muscular dystrophy
52
culturing cells can be done in what two ways?
suspension and solid surface
53
suspension is best for?
bacteria archaea and yeast
54
solid surface is best for?
most animal cells
55
what are two differences between suspension and solid surface media?
suspension:
- minimal media, inorgamic salts, carbon source, water
- faster growing
- contamination less of issue
solid surface:
- antibiotics added
- provide 9 essential amino acids
- vitamins, salts, fatty acids, glucose
- serum provides insulin, transferin and growth factors
56
In_______ media omly the temperature must be controlled while in _______ media temperature atmosphere and humity must be controlled
suspension, solid
57
_______ cells are isolated directly from tissue
primary
58
spontaneous oncogenic mutations lead to oncogenic _________
transformation
59
what type of cells are considered immortal and called a cell line?
transformed cells
60
aneuploidy is?
abnormal number of chromosomes
61
what are the 3 main steps to isolating cells?
1. lyse the cells
2. separate organelles based on key characteristics
3. use isolated organelles for further study
62
lysis means?
breaking open the cells
63
what are the 3 techniques used to disrupt the cell membrane?
high speed blending, sonication, and tissue homogenizer
64
swelling cells in a _________ solution weakens the plasma membrane making it easier to rupture.
hypotonic
65
passive transport is the movement of molecules ________ the concentration gradient
along
66
simple diffusion is?
allows molecules to freely cross the plasma membrane along the [ ] gradient
67
facilitated diffusion is?
channels and carriers, allows molecules to move through a membrane protein along the [ ] gradient
68
hypertonic solutions have a ____ solute concentration than the cell while hypotonic solutions have a _______ concentration than the cell
higher, lower
69
what is the homogenate?
after lysis a mix of suspended cellular componants
70
centrifugation separates particles based on _______ or ________
mass or density
71
sequential differential centrifugation?
yeilds fractions of organelles that differ in mass and density
72
equilibrium density gradient centrifugation?
separates cellular components by density
73
during differential centrifugation large cell fragments form the ________ while soluble proteins remain in the _______
pellet, supernatant
74
what is proteomic analysis?
can identify all protein components in a preparation of a purified organelle
75
monoclonal antibodies recognize what?
an organelle specific membrane protein
76
proteomic analysis requires 3 things
1. isolation at a high purity
2. method to identify all proteins in the organelle
3. genome sequence for reference comparison
77
what is the hematocrit?
volume of blood cells packed by centrifugation in a given volume of blood
78
what is flow cytometry?
machine flows cells past a laser beam that measures the light that they scatter and the fluorescence that they emit
79
in order to identify recombinant cells that are expressing GFP a good method would be?
flow cytometry
80
what is FACS?
fluorescence activated cell sorter, based on flow cytometry
81
what is this describing?
cells are mixed with a buffer and forced through a nozzle, droplets dont contain cells, some only contain one
FACS
82
separating white blood cells would be an example of ?
flow cytometry
83
monoclonal antibodies are made by?
identical clonal immune cells
84
what is monovalent affinity?
all bind to the same epitope
85
monoclonal antisera is?
single epitope recognized
86
polyclonal antisera is?
multiple epitopes recognized
87
what are hybridoma cells?
produce monoclonal antibodies that bind one antigen epitope and are used for basic research therapeutics
88
what is the target based approach for drug development?
start with target selected from biochemical pathway linked to specific disease state
89
in light microscopy _________ is limited by ________
resolution, wavelength
90
what are the 3 optical microscopes?
bright field, phase contrast, fluorescence
91
what is the most important property of optical microscopes?
resolution
92
what does "D" represent ?
distance between two objects, the smaller the D the better the resoluton
93
alpha represents what when calculating resolution?
angular aperture
94
N represents what when calculating resolution?
refractive index
95
what is the other limitation to light microscopy other than resolution?
light must be able to pass through the sample
96
chemical cross linking of proteins and nucleic acids and proteins is known as?
fixing
97
cutting parafin embedded tissue into 50nm thin slices is known as?
sectioning
98
dye certain molecules is known as?
staining
99
what is an HE stain?
uses hematoxylin and eosin
100
hematoxcylin binds to basic_____ _____ while eosin binds to ________ molecules
amino acids, acidic
101
how can an organism be classified as fluorescent?
if it absorbs light at one wavelength and emits light at a longer wavelength
102
green fluorescing dye is specifically bound to?
mitochondria
103
red fluorescing dye is incorporated into?
lysosomes
104
indirect immunofluorescence because the fluorochrome is on the _________ ____________
secondary antibody
105
what are the advantages of indirect immunofluorescence?
amplified signal, secondary antibodies are cheaper
106
do fluorochromes have to be attached to antibodies?
no
107
what are the two main drawbacks of fluorescence microscopy?
blurring of images causes by fluorescence outside plane of focus, cant visualize thick specimens
108
what is confocal microscopy?
illuminate and collect emitted fluorescent light from one small area of a focal plane at a time, collect many images and build up final figure
109
what improves image clarity by removing out of focus light?
deconvolution and confocal microscopy
110
what is FRAP?
fluorescence recovery after photobleaching
111
what is FRET?
forster resonance energy transfer
112
what is this describing?
starts with gfp tagged transmembrane protein in a cell, uses high intensity light to bleach gfp in a certain patch until it no longer fluoresces
FRAP
113
what is this describing?
measures distance between fluorochromes
FRET
114
what reveals protein interactions?
FRET
115
the short wavelength of electron microscopy high energy electrons yeilds ______ resolution images
high
116
what are the two main types of EM?
transmission electron microscopy and scanning electron microcopy
117
electrons pass through sample in?
TEM
118
electrons are scattered off sample in?
SEM
119
how does TEM work?
specimens are prepared before, tick material is fixed, dehydrated, plastic embedded, stained with electron dense heavy metals
120
how does SEM work?
metal shadowed material reveals surface features of specimens, molecules are excited and release secondary electrons that are focused into scintillation detector
121
which em method has less revolving power, SEM or TEM?
SEM
122
ampipathic phospholipids have ________ faces and ________ cores?
hydrophilic faces and hydrophobic cores
123
individual phospholipids spin and diffuse _______ within the plane of the membrane
laterally
124
how do we measure lateral diffusion?
FRAP
125
chain disorder _______ bilayer thickness
decreases
126
the cytosolic face always faces the _______
cytoplasm
127
the expolasmic face faces the _____ _________ or _______
cell exterior or lumen
128
what are two reasons membrane fluidity and flexability are important?
enables organelles to assume typical shapes
provides dynamic property that enables mebrane budding and fusion
129
when phospholipids are disperse in an aqueous solution they form what 3 things?
liposomes, micelles, and bilayer sheets
130
what are the phospholipid arrangements governed by?
hydrophobic affect
131
type of aggregate formed by phospholipids depends on?
temp, and length or saturation of fatty acyl tails
132
small polar head favours?
inverted micelles or cubic structures
133
similar polar head and hydrophobic region favours?
bilayers
134
bulky polar head and one acyl chain favours?
micelles
135
what are the most common phospholipids?
phosphoglycerides, derivatives of glycerol 3 phosphate
136
what are sphingolipids?
derivatives of sphingosine
137
the 3 sterols are?
cholesterol (animal)
ergosterol (fungal)
stigmasterol (plant
138
sterols are made up of?
polar head- single polar hydroxyl
tail- conjugated 4 ring hydrocarbon and short hydrocarbon chain
139
what are flipases used for?
for phospholipids to move between leaflets
140
sphingomyelin is synthesized where?
on expolasmic face of golgi complex
141
phospholipids are synthezised where?
cytosolic face of ER
142
cholesterol helps maintain______
fluidity
143
what are the 3 membrane proteins?
integral, lipid anchored, peripheral
144
what does this describe?
fatty acyl chains pack tightly against the hydrophobic outer surface of protein form shell around the protien and rearely exchange with other phospholipids?
annular phospholipids
145
what is the function of transmembrane helices?
guide assembly and stabalize multimeric membrane proteins
146
porins are found where?
in outer membrane of gram negative bacteria , mitochondria and chloroplasts
147
lipid anchored proteins can be attached to either the ___ or _____ terminus?
N or C terminus of polypeptide
148
what are two functions of phospholipases?
degrade damaged/ aged cellular membranes
generate signaling molecules
149
detergents are used for?
to solubilize lipids and membrane proteins
150
ion detergents contain a ____ _______ and do what?
charged group, denature protiens
151
non ionic detergents lack a charged group and do what?
extract transmembrane proteins in folded active form
152
when can detergents form micelles?
low concentrations but dissolce as isolated molecules
high concentrations form micelles
153
what is the critical micelle concentration?
breakpoint at which micelles form
154
light energy occurs in the ________ membrane of chloroplasts
thylakoid
155
what is the soluble portion of the chloroplast?
stroma
156
what occurs in light reactions?
associated with the thylokoid membrane,, capture light energy and convert it to chemical energy in the form of NADPH and ATP
157
what occurs in dark reactions?
located in the stroma uses NADPH and atp to drive the endergonic process of hexose sugar formation from co2
158
light reactions use ______ to capture solar energy
chlorophyl
159
chlorophyl is a ?
photoreactive isoprene based pigment
160
what is coordinated with the centre of the planar conjugated ring structure in chlorophyl?
mg2+
161
what confers membrane solubility in chlorophyl?
phytol
162
what are the 4 main steps of photosyntheis?
1. light absorption
2. electron transport and reduction of NAD+ and NADPH
3. synthesis of ATP
4. carbon fixation
163
where is DCPIP used?
etc reduces dcpip instead of NADP+
164
______ replaces the final electron carrier in photosynthesis?
DCPIP
165
where are phospholipids synthesized?
ER
166
what is the difference between saturated and unsaturated fatty acids?
fatty acids have no carbon carbon double bonds (saturated with H)
unsaturated fatty acids do have at least one C=C or triple bomds
167
what transports fatty acids?
cytosolic proteins, FABP
168
lipid transport is done by what 3 things?
vesicle transport, membrane bridges, lipid transfer proteins
169
a pure lipid bilayer is impermeable to what?
ions
amino acids
sugars
water soluble molecules
170
rate of diffusion across a pure phospholipid barrier is proportional to _________ ________, _______ and _______
concentration gradient
| hydrophobicity and size
171
what does a high K value mean when regarding diffusion?
greater fraction found in oil therfore more hydrophobic and faster to cross a bilayer
172
uniporters transport _____ molecule
1
173
symporter and antiporters transport _____ moleucles
2 molecules
174
atp powered pumps use what type of transport?
primary active transport
175
what forms of transport do not need energy?
simple diffusion
channels and uniporters (facilitated transport)
*** movement down gradient
176
what types of transport use energy?
symporters and antiporters (secondary active transport)
atp powered pumps (primary active transport)
*** movement up gradient
177
what is the fastest transport?
glucose transport
178
*what cell monomers form covalent bonds?
amino acids, nucleotides, phospholipds and monosaccharides
179
*the information dictating the proper folded conformation of a nascent protein is contained with?
primary amino sequence of the nascent protein
180
*proteins preform numerous functions including ?
- controlling protein activity (regulation)
- monitoring the environment and transmitting information (signalling)
- moving small molecules and ions across membrane (transport)
- catalyzing chemical reactions (enzymes)
181
*what would cause diploid yeast to form haploid yeast spores?
nutrient limitation
182
*what can occur when researches inactivate a gene in a model organism?
all of the above
abolish production of a protein encoded
study effects of loss of function
they can produce animal versions of human disease
they exhibit symptoms of disease in model organisms
183
*why can we not use bacteria to study organelle deficiencies in higher eukaryotes?
bacteria lack the organelles found in eukaryotes
184
*if a detergent was added to the homogenate what would happen?
cellular material would migrate randomly throughout the tube
185
*which enzyme would be the best marker for chloroplasts?
photosystem II
186
* transformed cells have a finite life span?
false
187
*hybridoma cells:
- grow rapidly
- are immortal
- produce monoclonal antibody
all of the above
188
* does the magnification of a microscope affect the resolution?
no
189
*an oil immersion lens is specialized to focus through a droplet of oil placed on top of the coverslip, which parameter is changed?
N, refractive index
190
* is detecting a FLAG epitope tag with a fluorochrome coupled anti flag monoclonal antibody an example of direct or indirect immunofluorescence?
indirect
191
*you have bright field light microscope and want to re tool it to make a fluorescence microscope. what parts do you need?
filter
192
*imagine you want to determine the location of a protien. your hypothesis is that the transmembrane protein is located in the mitochondria membrane. which technique would you choose?
any of the above
immunofluorescence, GFP, FLAG
193
*you need a control stain to detect mitochondria? what would you choose?
FLAG
194
*FRAP is based on?
the dynamics of proteins in a membrane
195
*what sample would transmission electron microscopy be the best choice?
internal structure of fixed cells
196
*for what sample is scanning electron microscopy the best choice?
surface structure of fixed cells
197
*which technique is best viewed for living unstained cells?
phase contrast
198
which membrane leaflet of the inner membrane faces the chloroplast stroma?
cytoplasmic face
199
*in a receptor mediated endocytosis what features end facing into the cytoplasm on the final coated vesicle?
clathrin
200
*what type of membrane protein is shown?
integral is throughout the cell
201
*what are common features of most integral membrane proteins?
hydrophobic alpha helices and one or two hydrophilic domains
202
*you wish to extract a transmembrane tyrosine kinase and assay its function. which of the following detergents would you use for the extraction?
octylglucoside
203
*you attempted to isolate chloroplasts and tested the results usin DCPIP. If purification of chloroplasts was innefective so that there was very little PSII present, what would occur?
DCPIP would remain blue
204
*chloroplasts?
all of the above
205
*what is not a challenge pertaining to phospholipid synthesis that cells overcome?
all are challenges
- lipid must insert into membrane
- many membranes cannot carry out lipid synthesis
- phosholipids cannot be transported by vesicles
206
*phospholipids and cholesterol are transported by what mechanisms?
all of the above, vesicular transport, direct, individual or carrier
207
*which bloodstream lioprotein trasnports the greatest proportion of cholesterol?
LDL
208
*would cells survive if their membranes were pure lipid bilayers?
nope
209
*active transport does not include?
diffusion and uniport
210
*pumps include?
atpases
