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Cell biology > Week 4 > Flashcards

Week 4 Flashcards

1
Q

modifications to amino acids

A

phosphate, acetyl, sumo, ubiquitin, methyl

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2
Q

proteins are NOT

A

long linear molecules of amino acids

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3
Q

primary structure of protein
secondary
tertiary
quaternary

A
  • amino acid sequence. linked by peptide bonds.
  • stretches of polypeptide chain. alpha helix, b sheet. backbone hydrogen bonding
  • polypeptide chain. interactions of R groups
  • more than one polypeptide chain. noncovalent bonds of different chains
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4
Q

C reactive protein

A

binds to C polysaccharide. Donut as protein, made up of five individual amino acid chains. but you need 5 to have a functional C reactive protein.

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5
Q

every protein wants to be at its

A

lowest energy state.

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6
Q

A (unit)

A

angstrom. length.

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7
Q

beta sheet (strands)

A

parallel or antiparallel, form H bonds bw side chains

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8
Q

proteins share similar structures

A

domains = sequence of amino acids w diff structure/function.

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9
Q

some proteins may add

A

domains over the course of time (duplications). may have multiple domains

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10
Q

SH3

A

binds polyproline regions

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11
Q

SH2

A

binds phosphorylated tyrosine residues (Y^P)

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12
Q

kinase domain

A

phosphorylates (adds) proteins (can be tyrosine kinase or ser/thr kinase{bc of hydroxyl groups}) or lipids. has catalytic activity.

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13
Q

when the protein is in tertiary structure

A

it is at its lowest energy state.

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14
Q

protein structure functions

A
  • regulates activity-temporal and spatial activation (when and where to act) depending on structure
  • specificity of activity- act on “correct” substrates based on structure
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15
Q

intracellular trafficking/vesicular trafficking

A

vesicles move cargo from one place to another

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16
Q

endocytic pathway

A

-Normal pathway - early endosome to late endosome to lysosome
– Decreasing pH is imp for protein-protein interactions

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17
Q

what do lysosomes do in cell?

A

break down molecules that are brought to site so it can be used for amino acids, carbohydrates (food sources).
-acid hydrolases - proteins that cut

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18
Q

exocytic pathway

A
  • Transport of molecules from inside cell to the plasma membrane or elsewhere
  • ER to ergic to golgi to EE - LE -LYS (PM)
  • known as secretory or biosynthetic pathway
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19
Q

vesicular transport
3 steps
vesicular ____ ?

A
  • vesicle budding - coat proteins
  • vesicle transport - rabs, tethers
  • vesicle fusion - SNARES
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20
Q

3 main COAT proteins

functions?

A

-clathrin (in PM and some in GOLGI (away from trans golgi)
-COPI coat- ERGIC and GOLGI
-COPII coat- ER to ERGIC
Functions
-formation of vesicle, causes curvature
-concentration cargo

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21
Q

what needs to be curved?

A

membrane needs to curve around cargo

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22
Q

Clathrin made up of what?

A
  • 3 large polypeptides and 3 small polypeptides chains

- Triskelion

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23
Q

underside of plasma membrane

A
  • Forms into basketlike structure called a coated pit

- Causes curvature and concentrates cargo

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24
Q

Clathrin doesnt act alone

A
  • adaptin binds to clathrin, membrane, and transmembrane proteins-to help get them into coated pits (Concentrates cargo)
  • Different adaptins used (AP1, AP2 and AP3)
25
why do we need 3 diff adaptin proteins?
all about specificity.
26
ligand
protein that binds to another protein. changes its shape and function.
27
protein that pinches off
clathrin and adaptin and dynamin
28
dynamin
wrapped around membrane, known as GTPase.
29
hydrolysis
cleave a phosphoanhydride bond
30
adaptin has a lot of
polypeptides. whole thing is macromolecular assembly.
31
GTPase
- Class of proteins - Utilize binding of GTP/GDP-changes in conformation - Binding to GTP turns “on” - Hydrolysis of GTP to GDP turns “off”
32
backwards- | forwards-
- retrograde | - anterograde
33
ergic can also be called
VTC-vesicular tubular cluster. From ERGIC, | vesicles bud and go to cisGOLGI
34
Sar1
is GTPase. binds to gtp and hydrolyzes gtp to gdp
35
ERGIC stands for
ER golgi intermediate compartment
36
what sec proteins make up COPII?
sec 13/31, sec 23/24
37
COPI
- Retrograde transport from ERGIC to cis GOLGI - Retrograde transport from TGN back to CGN - CGN back to ERGIC and ER
38
uncoating
- happens quickly after budding - requires ATP - coats are removed
39
when the clathrin and cargo buds off
it is called clathrin coated vesicle
40
GTPase cycle
hydrolysis of water loses an inorganic phosphate. cleaves GTP and leaves it in GDP bound form, and GAP proteins help to speed up cleavage.
41
GTPase cycle | how do you get it back to GTP?
enzyme that adds phosphate. GDP needs to come off so that GTP can bind. GEF bumps off GDP.
42
without gap and gef
goes really slow
43
GAP stands for
GTPase activating protein
44
GEF stands for
guanine nucleotide exchange factor
45
caax box
found at C terminus. (cystein, alanine, alanine,..). has to be there for lipid modification. Ccxx - caax box has 2 sequences
46
tethering molecules
loose interactions. low affinity.
47
Snares stands for what
snap associated receptor | high affinity.
48
rab proteins
- C-terminal end - spatial specificity. helps vesicle move from one location to another through tether molecules. - GDP lipid tail tucked in - GTP lipid tail sticking out
49
another name for late endosome
MVB. multi vesicular body
50
of rabs in human genome
70
51
snare proteins
- Coiled-coil proteins - Bind in a 1:3 ratio of coils - v-SNARE and t-SNARE - R-SNARE (almost always v snares) and Q-SNARE (almost always t snares) - SNARE promiscuity - bind with many different SNARES in vitro
52
in vitro
outside of its natural place.
53
mechanism of SNARE fusion
Docking Zippering Membrane fusion Cis-SNARE complex must be dissociated to regenerate trans-SNARE proteins
54
rabs are in
endo and exocytic pathways
55
delivery to lysosomes in 3 ways
- phagocytosis-cells eat - autophagy- cells eat oneself - receptor mediated endocytosis
56
lysosomes cut what?
- protease-cuts proteins - lipases- lipids - glycosilase- glyocprotiens - nucleases - nucleic acids
57
autophagy
removal of damaged organelles. membrane surrounds it, then delivered to lysosomes where it will be degraded
58
protein get modified
addition of sugars or phosphate
59
in the fusion step (SNARE), you need ____ to cleave off the cis snare complex so you can reuse it
NSF and ATP

Cell biology (15 decks)

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