Midterm 1 Flashcards
1
Q
What are proteins made of?
A
Amino Acids
2
Q
What are nucleic acids made of?
A
Nucleotides
3
Q
What are polysaccharides made of?
A
Carbohydrates
4
Q
What are lipids made of?
A
Fatty acids
5
Q
What are the four main types of macromolecules?
A
Proteins, Nucleic Acids, Polysaccharides, and Lipids
6
Q
All macromolecules are built from monomers except for?
A
Lipids
7
Q
What is an oligosaccharide?
A
A small chain of monosaccharides?
8
Q
What is a fat made of?
A
A fat is a triglycerol: made of 3 fatty acid tails, and one glycerol
9
Q
What is the difference between a phospholipid and a fat?
A
Phospholipids have 2 fatty acid tails and fats have 3 fatty acid tails.
10
Q
A fatty acid is composed of….
A
Hydrocarbon chains (hydrophobic) and a carboxyl group (hydrophilic)
11
Q
Fats, steroids, and phospholipids are all examples of…
A
Lipids
12
Q
Describe the structure of a steroid
A
4 hydrocarbon rings with a hydroxyl group attached to one of the rings
13
Q
What are the 3 types of proteins?
A
Enzymes, structural, and regulatory
14
Q
How do amino acids hook together?
A
Peptide bonds
15
Q
What is an amino acid formed of?
A
An amino group, alpha carbon, hydrogen ion, carboxyl group and a side chain (R group)
16
Q
What gives an amino acid its determining characteristics?
A
The R group
17
Q
What is a peptide?
A
A short chain of amino acids
18
Q
What is a protein?
A
A folded polypeptide
19
Q
Describe the four levels of structures
A
1) Primary: linear strain
2) Secondary: alpha helix
3) Tertiary: folded alpha helices
4) Quaternary: group of tertiary structures
20
Q
What is the function of Ribonuclease A?
A
Digest RNA
21
Q
What is a molecular chaperone?
A
A protein that binds to another to protect it by changing it’s shape
22
Q
Why are cells compartmentalized?
A
Separate functions, prevents random movement through membrane, protect from outer activities
23
Q
What are some membrane functions?
A
Provide selective barrier, help with cell to cell interactions
24
Q
What are membranes composed of?
A
Lipids, Carbs, Proteins
25
_____ makes up most of membrane lipids
Phospholipids
26
Up to __% of the membrane can be composed of cholesterol.
50
27
Lipids are easily able to switch places side by side but in order to flip they require help from membrane proteins containing _____.
Flippase
28
Why do holes in the lipid bilayer seal almost immediately?
Because hydrophobic tails become exposed so lipids move together to prevent water touching the tails
29
How do carbs attach to the membrane?
Binding covalently to lipids or proteins
30
All carbs are either ___ or ___ linked
Nitrogen, Oxygen
31
Carbs never face ___ the cytoplasm
Into
32
What does asymmetric mean in terms of the membrane?
Something can be attached to one side of the membrane but not the other
33
What is the difference between integral and peripheral proteins?
Integral proteins are embedded in the membrane, and peripheral are blinded to the outside/inside layer of the membrane
34
How are peripheral proteins attached to the membrane?
to integral proteins via electrostatic bonds
35
What is a GPI anchored protein?
A protein that is bound to a lipid
36
What are the four features of the fluid mosaic model?
asymmetric, embedded, mosaic, and quasifluid
37
What are the 3 types of membrane lipids?
Glycolipids, Phospholipids and Cholesterol
38
Are peripheral proteins hydrophilic, hydrophobic or amphipathic?
Hydrophilic
39
What is a sphingolipid?
Long chain hydrocarbons come together in membrane, pack tightly and become gel like, like a lipid raft
40
What is a lipid raft?
Tightly packed lipids/cholesterol in a patch on the membrane outer leaflet where GTI proteins can attach
41
The ____ is central to the microtubules
Mitochondria
42
What is metabolism?
collection of all biochemical reactions
43
The ___ pathway takes complex structures and breaks them into smaller components so the molecules can be reused. Produces energy
Catabolic
44
The _____ pathway takes simple components and builds more complex ones by using energy
Anabolic
45
What are a few functions of the mitochondria?
Synthesizing amino acids, calcium transport
46
What is the function of Drp1
binds/hydrolyzes GTP, involved in splitting mitochondria in half
47
What is the crust and where is it located?
in the inner membrane, increases SA
48
What is the inter membrane?
located between the inner and outer membrane
49
What is a porin?
A major protein channel in the mitochondrial membrane allowing ATP transfer when open. Located in outer mitochondrial membrane
50
Does the inner membrane contain more protein or more lipids?
3-4 protein: 1 lipid
51
___ is the loss of electrons and ___ is the gain of electrons
oxidation, reduction
52
What is glycolysis?
the pathway of glucose oxidation
53
What is produced by glycolysis?
pyruvate, 2 ATP, 2 NADH
54
NADH accepts _ é and _ H+
2, 1
55
What is NADH?
A co-factor
56
Pyretic Acid + Co A + NAD ->
Co A + 2 C chain + NADH + CO2
57
What is pyruvate broken down into?
acetyl group, 2e, 2 H+, CO2
58
What do you get as products in the TCA cycle?
CO2, NADH, FADH2, GTP, Oxaloacetic acid
59
Cells cannot use electrons as energy, it must be converted into ?
ATP
60
____ reacts with acetyl Co A to start the TCA cycle again
Oxaloacetic acid
61
How many times does the TCA cycle occur for every molecule of glucose?
2
62
What is oxidative phosphorylation?
The formation of ATP driven by the transfer of é to oxygen
63
What is the electrochemical gradient?
change in voltage/concentration across the membrane
64
What is chemiosmosis?
the production of ATP using the energy of H+ gradients across membrane to phosphorylate ADP
65
2,4-dinitrophenol inhibits chemiosmosis by?
Uncoupling é transport and ATP synthesis
66
What are the four main organelles that are part of the endomembrane system?
Golgi, ER, Endo/Lysosomes
67
What is the function of the endomembrane system?
Involved in synthesizing membranes and moving stuff around
68
Which side of the ER membrane contains ribosomes?
Cytosolic side
69
What are the functions of the sER?
Synthesis of steroid hormones, detoxification, and sequestering calcium
70
Where are the proteins synthesized?
Ribosomes
71
What is cell fractionation?
A technique used to show that free ribosomes make different kinds of proteins than membrane bound ribosomes
72
What experiment was used to examine the secretion pathway?
Pulse Chase Experiment
73
What is a yeast sec mutant?
yeast with degenerative genes which synthesize secretory proteins but won't secrete the proteins
74
Yeast sec will secrete proteins at room temp but will stop secreting proteins when the temp is ____.
increased
75
What happens when mRNA is translated?
protein is created
76
Proteins can accumulate in which 5 places which can block the secretion pathway?
2x Vesicles, Cytosol, ER, Golgi
77
What does a signal recognition particle do?
binds to signal sequence on ribosome causing translation to stop and elongation of polypeptide to occur
78
How does the cell know if a protein should be inserted into the membrane?
Amino end of protein has signal sequence telling it would be inserted into the membrane
79
What side of the ER membrane has the signal sequence receptor on it?
Cytosolic side
80
What is a translocon?
a group of integral membrane proteins and SPP complex that forms a channel
81
How does con translational translocation mechanism work?
Protein is synthesized by hydrophobic amino acids as it goes through the membrane. Stop sequence forms, hydrophobic part secreted into membrane
82
What are the names of the 2 leaflets of membrane?
cytosolic, exoplasmic
83
Why are lipids difficult to synthesize in the cytosol?
because of the hydrophobic tails
84
What is the function of flippase?
flippase flips lipids from one leaflet of membrane to the other because integral membrane proteins only produce lipids into one leaflet of the membrane so in order for both layers to grow, the material from one leaflet must be flipped to the other side
85
How are lipids transferred through the cell?
Proteins bin to them covering hydrophobic bits
86
What is an O-linked protein?
A protein that attaches to serine/theronine
87
What is an N-linked protein?
a protein that attaches to asparagine
88
Where does O-linkage occur?
Golgi
89
Where does N-linkage occur?
ER/Golgi/ERGIC
90
What is the function of Dolichol Phosphate?
moves sugar around membrane
91
How many sugars can a dolichol carry at once?
7
92
What does oligosaccharyltransferase do?
transfers sugar/dolichol chain into an asparagine covalent linkage
93
What is the point of quality control?
allows cell to select/destroy misfiled protein
94
What are the names of the 2 ER proteins responsible for quality control?
Calnexin and Calreticium
95
What is the function of calnexin?
Cuts off glucose and tries to fold it correctly
96
What is the function of calreticium?
binds to protein by glucose, cuts glucose off and protein is released
97
What does the enzyme UGGT do?
detects if proteins are folded correctly by checking if hydrophobic regions are exposed to lumen. Then it cuts off the mannose of proteins until it can no longer fold and a proteasome will destroy it.
98
What is the function of a proteasome?
protein machine that destroys other proteins
99
What are proteolytic enzymes?
enzymes that destroy proteins
100
What is ubiquitin?
a signal for the protein to be destroyed, threads protein into proteasome channel
101
What attaches ubiquity to the protein?
ubiquitin ligase
102
What happens to a cell containing too many misfiled proteins?
It will die (apoptosis)
103
What is the function BiP?
Once cell realizes a protein is misfiled. BiP tries to refold the protein
104
What is the function of the translation factor ELF2 Alpha?
turns of protein translation so bad proteins aren't made
105
What is apoptosis?
programmed cell death
106
What is the endoplasmic reticulum Golgi Intermediate Compartment(ERGIC)?
Space between the ER/Golgi
107
What are 3 regions of the Golgi complex called?
cis/medial/trans cisternae
108
The __ cistern is closest to the ER while the __ cisternal is closest to the plasma membrane.
Cis, Trans
109
Where are proteins usually modified?
Golgi, Integral Membrane Proteins
110
What are the 2 ways that stuff moves through the Golgi?
Vesicular transport, Cisternal Maturation model
111
What is the difference between vesicular transport and the cisternal maturation model?
CMM: retrograde, no vesicles
VT: vesicles, anterograde
112
How do vesicles break off of the organelle?
protein on surface coating of vesicles forces membrane to curve which causes the vesicle to snap off of the organelle.
113
What do COP2 coated vesicles do?
Move via anterograde to ERGIC/Golgi from ER or form cis to trans
114
What do COP1 coated vesicles do?
Move via retrograde from ERGIC/Golgi to ER or from trans to cis
115
What do clathrin coated vesicles do?
Move from trans Golgi network to endo/lysosomes and from PM to cytoplasmic compartments
116
How are ER proteins secreted?
Vesicles bud off of ER
117
What are the functions of a coated vesicle?
help shape vesicle, help select which proteins need to be moved
118
What does Sar1 do?
regulatory protein, responsible for formation of COP2 vesicles
119
How does COP2 get rid of its coat?
when the vesicle finds its desired location, GTP is hydrolyzed to GDP making the coat fall off
120
What is retention?
"if a protein is supposed to be in the ER than it stays in the ER" keeping what is meant to stay
121
What does ARF1 do?
regulatory protein responsible for formation of COP1 vesicles
122
What is retrieval?
retrieving a vesicle that took the wrong proteins to the wrong place, COP1 takes them back
123
What kind of protein recognizes if there is an incorrect protein in a vesicle?
Transmembrane proteins
124
What is the KDEL sequence at the end of a protein?
Lys-asp-glu-leu
125
What is the function of a lysosome?
destroys parts of cell that are no longer needed
126
How many enzymes do lysosomes contain?
50 works best in low pH
127
How do enzymes not destroy the lysosome?
lumen inside of membrane is very glycosylated which protects the membrane
128
How do lysosomes know when to destroy cell part?
Autophagosome surrounds organelle, lysosome binds to autophagosome and destroys the organelle
129
How are lysosomal enzymes taken to the lysosome?
coated vesicles from ER take them there
130
How do particles in vesicle get to target membrane?
vesicle membrane bind
131
What is tethering?
fibrous proteins tether vesicle to target
132
What do rabs do?
bind to GTP, help with tethering
133
What is docking?
fibrous proteins pull vesicle tighter and eventually fuse
134
The proteins on membrane and vesicles that determine where they go are called?
t/v-SNAREs
135
What are the 2 types of t SNAREs
syntaxin, SNAP 25
136
What is the name of a v-SNARE
synaptobrevin
137
What do SNAREs do?
bring vesicle closer to membrane via helical complex
138
What is the function of the NSF?
binds to SNARE complex and break it apart allowing t/v membranes to form together making a pore
139
What is a ligand?
anything taken into cell by endocytosis
140
There is a concentration of _____ that forms on a coated pit
LDL: Low density lipoprotein cholesterol
141
Describe the composition of clathrin?
3 heavy chains, 3 light chains, in Triskelion shape
142
The cytosolic membrane of a vesicle has one layer of ___ and one layer of ___ ___
clathrin, adapter proteins
143
What kind of structure does an adapter protein have?
quaternary
144
What is GTPyS
a kind of nonhydrolyzable GTP
145
What does Dynamin do?
hydrolyzes GTP causing conformational change in neck region of clathrin
146
What do house keeping receptors do?
bind to things cell needs
147
What do signalling receptors do?
bind to info containing molecules
148
What is endocytosis?
movement from outside cell to inside cell
149
Why would a cell want to degrade signal proteins?
to prevent over stimulation
150
Where does postranslational uptake of proteins occur?
nucleus, mitochondria, peroxisomes, and chloroplast
151
Name the 4 mitochondrial compartments?
Inner/outer membane, Inter membrane space, matrix
152
What is required to transfer a protein into mitochondria?
a transfer sequence telling the mitochondria to take in the protein
153
Describe the function of chaperone proteins?
affect the folding of other proteins, no structural info, recognize unfolded proteins, help them find their tertiary structure, require energy
154
Why are mitochondrial DNA synthesized in the nucleus?
Because they have encoded DNA
155
The ___ doesn't make any mitochondrial proteins so it gets its proteins from the _____
mitochondria, nucleus
156
Hsp 60 and Hsp 70 are examples of....
Chaperone proteins
157
Hsp 7 interacts with proteins made in ____ to assist in _____
cytosol, folding
158
What makes protein unfold in the matrix?
Hsp60/70, requires energy, chaperone hydrolyzes ATP, folds protein, pulls into matrix
159
What are amino acids made of?
A carboxyl group, amino group and side (r) chain
160
Carbs only attach to the _____ leaflet
exoplasmic
161
What kind of proteins are Myristate and Farnesyl?
GPI anchored proteins
162
____ is involved in membrane fluidity
Cholesterol
163
___ _____ move as a unit
Lipid rafts
164
Where are F1 particles located?
the inner mitochondrial membrane
165
Where does glycolysis take place?
The mitochondria/cytosol?
166
What is the purpose of the proton motive force in the case of this class?
Drives synthesis of ATP by chemiosmosis
167
What is 2,4-dinitophenol?
Passage ways in membrane for H+ to travel across
168
What does the F1 Complex (ATPsynthase) do?
changes ATP to ADP + Pi
169
Which unit of the binding change mechanism is the rotating unit?
Gamma
170
The beta subunits of the binding change mechanism are always in different conformations which are:
tight, loose, open
171
Microbodies, Peroxisomes, Glyoxysomes are all similar to...
the mitochondria
