Biology Flashcards
(120 cards)
1
Q
membrane proteins
A
have little hydrophobic stretch
- so biophysical force keeps them in hydrophobic core of membrane
- alpha helix of 20 AA
lipid anchors - attach some proteins to membrane
need to be folded properly before acquiring the functional state
2
Q
lipid bilayer
A
- connector group
- 2 hydrophobic tails
- hydrophilic head
3
Q
cholesterol
A
sits between membrane lipids
- used to position other membrane lipids in different way
4
Q
lipid rafts
A
- places where certain membrane proteins can self-organize
- because they don’t want to be in thick part of membrane
- post-synthetic modifications of membrane lipids
5
Q
soaps
A
similar to membrane since they both have hydrophobic and hydrophilic part
degrade membrane of microorganisms and make contents get out of cell
- then soap organizes itself as a sort of replacing of membrane lipids
once you isolate membrane protein
- purify it and bring it back in a system
6
Q
bacteriorhodopsin
A
can be used as capacitor
it is a membrane protein
constituted by 7 alpha-helices domains
- transports proton across membrane spending energy
7
Q
mitochondria
A
double membrane
due to production of oxygen (toxic) they were born to deal with it
have their own DNA and ribosomes
can undergo fission and fusion
derived from egg with no recombination
endosymbiotic theory
8
Q
endosymbiotic theory
A
they got engulfed by ancient eukaryotic cells
lost some of their genes that were already present in nucleus
9
Q
energy conversion
A
creation of proton gradient
ATP has strong bonds between phosphates that, if broken, release high energy
a lot of energy is derived from letting H combust with oxygen
- produces water and CO2
the cristae are needed to have enough membrane to allow hydrogen pumping and create hydrogen gradient
10
Q
krebs cycle (energy conversion)
A
takes place in matrix
protons are pumped out in inter membrane space
at end:
NADH –> NAD+
ADP –> ATP
11
Q
electron transport chain (ETC)
A
way of slowly making use of energy that is stored in high-energy electrons
in 3 stages, proton pumped across membrane
12
Q
bacteria flagella
A
a rod can turn thanks to proton gradient
created by ETC
- allows flagellum to turn around
13
Q
chloroplasts
A
3 membranes
- inner
- outer
- thylakoid
2 photosystems
- light is used to have carbon fixation
water + CO2 + energy => proton gradient => chemical energy
14
Q
secretory/exocytic pathway
A
ER –> Golgi –> Endosomes
endosomes turn into lysosomes and extracellular environment
15
Q
smooth ER
A
also produces cholesterol
lipid synthesis
produces ceramics by condensing serine with a FA to form sphingosine
then second FA is added
then transported to Golgi to form glycosphingolipids and sphingomyelin
16
Q
lipid synthesis
A
catalyzed by enzymes with active sites that face the cytosol
spontaneous flip-flop thanks to phospholipidic translator scrambles
flippases recognize the phospholipids that contain a free amino group in their head to transfer them to cytosolic leaflet
- thanks to energy of ATP hydrolysis
17
Q
rough ER
A
translocon
co-translational translocation
post-translational translocation
post-translational modifications
hydrophobic start-transfer and stop-transfer signal sequences may also act as transmembrane actors
18
Q
translocon
A
4 sec61 complexes
other complexes like oligosaccharide transferase and signal peptidase
19
Q
co-translational translocation
A
protein enters lumen while being synthesized by ribosome
SRP pauses translation
- when receptor on ER membrane binds to complex = released
20
Q
post-translational translocation
A
chaperons are needed to make the protein enter the lumen
this needs ATP
21
Q
post-translational modifications
A
cysteine will form intra- and inter-chain disulphide bonds
N-glycosilation of residues Asn-X-Ser and Asn-X-Thr by oligosaccharyl-transferaase
- this helps protect the walls of cell
22
Q
coated vesicles
A
clathrin-coated - transport from the Golgi and plasma membrane
COPI-coated - transport from Golgi to ER
COPII-coated - from ER to Golgi
- Sar1-GDP binds to Sar1-GTP that binds to Sec24 and Sec23
- happens when cargo receptor recognizes the cargo in ER
23
Q
Golgi
A
main function - digosaccharides processing
- each part dedicated to specific function
complex digosaccharides
high-mannose digosaccharides
golgins
constitutive secretory pathway
regulated secretory pathway
24
Q
golgins
A
protrusions that guide and monitor the vesicles of retrograde and anti-retrograde pathway
25
constitutive secretory pathway
soluble proteins, plasma membrane lipids and proteins are brought to cell surface
26
regulated secretory pathway
high specialized substances in highly specialized cells
- released when extracellular signal stimulates fusion of vesicle with plasma membrane
27
fusion of membranes
transmembrane coiled proteins between vesicle and target membrane, snare, wrap around each other
membranes get close + fuse together SO content in vesicle will get out of cell
(similar to what viruses do)
28
direct and indirect sorting
direct - parts of Golgi are dedicated to specific molecules
indirect - all proteins are directed to same point
- then transported to the correct domain
29
extracellular signaling distances
contact dependent
paracrine
autocrine
synaptic
endocrine
30
contact dependent
- molecules remain bound to surface of signaling cell
- influence only cells that contact it
31
paracrine
molecules are local mediators
- only act on cells near environment
32
synaptic
neuron, activated from other nerve cells, sends electrical impulses along axons
when it reaches synapse, triggers secretion of chemical signals that act as neurotransmitters
33
endocrine
cells secrete hormones into bloodstream
- so molecules are carried as far as they need
34
autocrine
cell produce signal that act on cell itself
35
transmembrane proteins
receptors on the cell's surface that become active when ligands bind to them and generate multiple signals
36
intracellular proteins
signals must enter the cell
- so needs to be sufficiently small and hydrophobic to diffuse across lipid bilayer
37
classes of receptors
ion channel coupled
enzyme couples
G-protein couples (GPCRs)
38
ion channel coupled
transmembrane proteins involved in rapid synaptic signaling between nerve cells
opening and closing of them are mediated by neurotransmitters
39
enzyme coupled
single-pass transmembrane proteins with ligand-binding site outside the cell while their catalytic site inside
40
G-protein coupled (GPCRs)
indirectly regulate the activity of another plasma membrane-bound target protein
trimeric GTP-binding protein mediates the interaction between activated receptor and target protein
- can change concentration of one or more small signaling pathways
41
intracelular signaling molecules
second messengers
diffuse from their source and spread the signal to other parts of cell
- water-soluble => cytosol
- lipid-soluble => plasma membrane
GTP binding proteins
molecular switches
- activated by phosphorylation by kinase and deactivated by dephospho rylation by phosphatase
--> kinase cascade
42
GTP binding proteins
- G proteins - send signals from GPCRs that activate them
- monomeric GTPases - send signals from many types of cell-surface receptors
43
regulatory proteins
GAPs (GTPase-activating proteins)
- trigger GTP hydrolysis and deactivate proteins
GEFs (guanine nucleotide exchange factors)
- promote the release of bound GDP
- to allow GTPs binding
44
intracellular signaling complex
scaffold proteins
- group interacting signaling proteins into signaling complexes
signaling complexes
- form temporarily in response to a signal and disassemble when that signal is gone
phosphoinositides
- modified phospholipid molecules in adjacent plasma membrane that recruit specific intracellular signaling proteins to these regions to activate them
45
intracellular signaling interactions
when induced proximity isn't sufficient to activate proteins we rely on interaction domains
if proteins only have a few interaction domains, they're adaptors
- and link 2 other proteins together in signaling pathway
46
interaction domains
Src homology 2 (SH2) - binds to phosphorylated tyrosine
phosphotyrosine-binding (PTB) - binds to phosphorylated tyrosine
Src homology 3 (SH3) binds to proline-rich AA sequences
Pleckstrin homology (PH) - binds to charged heads of phospholnositides
47
response
speed depends on the molecules that carry it out
- and temporary extracellular signals often produce lasting effects
- sigmoidal or discontinuous
strong positive feedback can generate an all-or-none, self-sustaining response
negative feedback limits level of response
48
GPCRs
single polypeptide chain that threads back and forth across lipid bilayer 7 times
when activated becomes a G protein
49
cyclic AMP (cAMP)
synthesized from ATP and adenylyl cyclase
rapidly destroyed by cAMP phosphodiesterase that hydrolyze it to 5'-AMP
activated by signals that activate GPCRs coupled to stimulatory of G protein that activates adenylyl cyclase
activates cAMP-dependent protein kinase (PKA) that phosphorylates specific series or threonine on target proteins => regulating their activity
50
phospholipase C-B (PLCb)
activated by G protein Gq
- acts as PIP2
cleaves PIP2 to generate:
- IP3
- diacyglycerol (activates PCK combination with Ca2+)
51
Ca2+
when Ca2+ rushes into cytosol, it increases the local concentration 10-20 folds
- activates Ca2+ responsive proteins
can enter through IP3 receptors or ryanodine receptors
if extracellular signal is strong, Ca2+ oscillations can occur
52
calmodulin
is a multi-purpose intracellular Ca2+ receptor that consists in highly conserved single polypeptide chain with 4 high-affinity Ca2+ binding sites
to activate it
- needs a lot of Ca2+ so it acts as a switch to increase Ca2+ conc.
53
olfactory receptors
when stimulates => activate a specific G protein, Golf, that activates adenylyl cyclase
the increase in cAMP open cAMP-gated cation channels
- allows an influx of Na+ which depolarizes the olfactory receptor neuron and initiates a nerve impulse
54
visual receptors
similar process but with cGMP
synthesis - guanylyl cyclase
degradation - cGMP phosphodiesterase
rods and cones
55
rods (rod phosphoreceptors)
contain rhodopsin disks in outer segment
1. light comes
2. forces conformational change in protein (opsin) that alters conformation of G protein transfusing (Gt)
3. causes the transfusing alpha subunit to activate cGMP phosphodiesterase that hydrolyzes cGMP
4. closes channels and inactivates the rods
56
nitric oxide
neurotransmitter acetylcholine stimulates GPCR that induces NOS to synthesize NO
relaxes smooth muscles of walls of blood vessels
eNOS - endothelial
nNOS - nerve and muscle cells
iNOS - inducible
57
desensitization
receptor inactivation - altered so they can't interact with G proteins
receptor sequestration - temporarily internalized to not have access to ligand
receptor down-regulation - destroyed in lysosomes after internalization
58
enzyme couples receptors
transmembrane proteins with their ligand-binding domain on outer surface of plasma membrane
receptor tyrosine kinases (RTKs) phosphorylate selected tyrosine side chains
intracellular signaling molecules share highly conserved phosphotyrosine-binding domains
- SH2
- PTB
59
RAS family
monomeric GTPases that relay signals from cell surface receptors
- can spread them along downstream
active form (RAS-GEFs) and inactive form (RAS-GAPs)
60
PI 3-kinase
phosphorylates inositol phospholipids
promotes cell survival and growth
PI can undergo reversible phosphorylations => phosphoinositides
serves as a docking site for various intracellular signaling molecules
PI-3-kinase-Akt - depends on protein kinase TOR:
- mTOR1: stimulates cell growth and promotes cell survival
- mTOR2: helps activate Act and regulates the actin cytoskeleton via Rho family GTPases
61
cytokine receptors
local receptors associated with cytoplasmic tyrosine kinases (JAKs)
- they phosphorylate and activate transcription regulates (STATs)
dimers or trimmers associated with few JAKs that phosphorylate each other to form phosphotyrosines that will bind to STAT through SH2 domains
62
transforming growth factor-B family (TGF-B)
dimeric local mediators that act through enzyme-couples receptors with a serine/threonine kinase domain on the cytosolic site
type I - phosphorylates latent transcription regulator of Smad family
type II - phosphorylates types I
negative feedback
- Smad 7 competes with R-Smad and decreases its phosphorylation
- Smad 7 recruits the ubiquitin ligase Smurf => internalization and degradation
63
notch receptor
role in production of Drosophila neural cells
single pass transmembrane protein that requires proteolytic processing
1. activated by Delta
2. plasma membrane-bound protease cleaves off tail that translocates into nucleus
3. to activate transcription of Notch-response genes
64
WNTs
unusual secreted protein because of FA chain increases their binding to cell surface
WNT/B-catenin pathway
planar polar pathway
if absent, responsive genes are kept silent by an inhibitory complex form by protein of LEF1/TCF family bound to a co-receptor protein of Groucho family
65
hedgehog proteins
encoded by genes Sonic, Desert and Indian hedgehog
- if active, covalently coupled to cholesterol or to FA chain
mediated by latent transcription receptor cubits interruptors (Ci)
- phosphorylated by PKA, GSK3 and CK1
when there's a signal, 3 transmembrane proteins block the proteolytic processing
- patched
- iHog
- smoothened
66
NFKB proteins
latent transcription regulators of innate immune response
activated by Toll, Toll-like, tumor necrosis factor alpha and IL1 receptors
5 of them:
- RelA
- RelB
- c-Rel
- NFKB1
- NFKB2
that form dimers
67
steroid hormones
cortisol
steroid sex hormones
vitamin D
thyroid hormones
retinoids
68
cortisol
produced in cortex of adrenal glands
influences the metabolism of cells
69
vitamin D
synthesized in the kinin response to sunlight
regulates Ca2+ metabolism
70
thyroid hormones
increase metabolic rate of cells
71
retinoids
made of vitamin A
local mediators in vertebrae development
72
singer sequencing method
1. single stranded DNA is put in mixture of nucleotides
2. some of them without -OH so that could stop sequence
3. when ddATP is inserted, DNA polymerase will stop the cain where A base was used
4. this is then repeated with all nucleotides (ddTTP, ddGTP, ddCTP)
73
restriction enzyme
can cut DNA between G and A
disrupts virus' DNA
DNA parts can be glued together through DNA ligase
- creates recombinant DNA
ex. used for insulin
74
polymerase chain reaction (PCR)
through DNA polymerase of bacteria that survives at boiling temp
keep synthesizing new strands of same DNA
- by lowering temperature after each time to anneal 2 oligonucleotide primers
- then rising it again to melt chains
if you need to start from RNA
- first make it into DNA through reverse transcriptase to form cDNA
75
homologous recombination
uses sequences that have overlapping stretches of DNA with whatever is in the genome of organism
76
transposable element
you can change all genes in genome and make trans gene or knockout
77
knockout mouse
cre lox system
- cre is an enzyme that removes the target gene only there's a lox site
you can target specific genes in order to have point mutation, recombination or removal of gene
78
DNA microarray
created to analyze simultaneously thousands of RNAs
1. composed by glass microscope slides that contain DNA fragments that serve as probes from mRNA produced by specific gene
2. extract mRNA and convert them into cDNAs that are fluorescently labelled
3. automated fluorescence microscope determines which mRNAs were present in sample based on where cDNAs are bound
4. epi maps are creates
- genes are given a color code depending on their up- or down-regulation
79
ribosomes profiling
1. isolate ribosomes
2. cut off RNA sticking out of them
3. covert DNA to RNA protected in ribosome
4. to determine its sequence
5. cells can change their translation pattern
80
epistasis analysis
studies how genes interact
81
CRISPR/CAS9
CRISPR system - causes short fragments of viral DNA to become integrates into genome
1. viral DNA sequences are integrated into CRISPR loci at 5' end
2. CRISPR locus is transcribed to produce long RNA molecule
- processed into shorter crRNAs
3. crRNAs + Cas9 protein seek out viral cDNA to be destroyed by nucleases
82
embryonic stem cells
can differentiate any cell line thanks to transcription factors
83
cells immortalization
starting from tumor cell and letting it fuse with normal cell
- you will get new cells that proliferate indefinitely
84
cell sorting
1. cell suspension
- separation of cells through enzymes in buffer solution
2. cells are put in cell sorter
- analyzes different shapes
3. light source shines light through solution
4. detector analyses specific characteristics
5. electric field breaks cells into tiny droplets and pulls them to different sides
85
antibodies
produced by plasma cells derived from B cells
to recognize them you need primary antibodies produced by host organism
polyclonal
monoclonal
86
monoclonal antibodies
always bind to same epitope
produced through hybridoma technique
1. inject mouse with antigen
2. B cells produce antibodies against it
3. take B cells and fuse with tumor B lymphocytes
4. gives us hybridoma cells
5. grow and make identical antibodies
87
polyclonal antibodies
act against antigens by identifying different epitopes on them
88
centrifuge
separate substances based on their mass or on how they would permeate through certain barrier
low speed
medium speed
high speed
very high speed
89
column chromatography
separate biological samples into fractions based on differential absorption of compounds to absorbent
90
ion-exchange chromatography
introduce in a solution positive beads
so negative components of the sample will stick to them
go out of solution later than positive
91
gel filtration chromatography
presence of beads with pores makes small particles to go out later
92
affinity chromatography
separates molecules depending on their affinity to the beads
its useful to purify biomolecules and proteins
93
electrophoresis
proteins travel through gel towards an anode
- bigger proteins are slower
SDS is negatively charged molecule that binds to positive charged proteins to make them negative
B-mercaptoethanol - used to break disulfide bonds so that proteins won't be fully stretched
94
pathways of UPR
IRE1
PERK
ATF6
95
IRE1
transmembrane protein kinase
target XBP1
96
PERK
inhibits translation initiation factor phosphorylating it
reduces production of new proteins
activates ATF4 that blocks translation
97
ATF6
transcription regulator
- when misfiled = proteins accumulate in ER, goes to Golgi
then can go to nucleus
98
B lymphocytes
may need to increase their secretory capacity so ER has to expand
- plasma cell
99
DTT
blocks disulfide bond formation in ER
100
LAC Z
chaperones promoter that encodes for B-galactosidase
101
CH1 domain
where Bip binds to light chains teams up with heavy chain
102
HAC1
has RNAase domain
digests mRNA so intron is removed and protein can act as transcription factor
in yeasts - XBP in human cells
103
ERAD
ER associated degradation
in cancer, the stress helps the disease to survive
- so UPR can send cells into apoptosis and reduce cancer
104
lazy UPR
stress response takes place too late
ex. UAKO
105
trigger happy UPR
response is quick even with few stress
ex. diabetes
106
charcot marie tooth neuropathy
due to lack of serine 63
myelin protein PO or MPZ misfiles in Schwann cells of peripheral nerves
protein accumulates but GAP34 blocks PERK activation and action
107
BIP
important chaperone
108
calreticulin (CRT)
chaperone located in reticular network of cell where heavy chains accumulate
109
PDI
another important chaperone
110
RIDD
RNA activated if IRE1 is over expressed
it is cytotoxic and drives towards apoptosis
111
origin of organelles
invagination of plasma membrane
endosymbiosis
112
invagination of plasma membrane
ancient prokaryotic cell invaginated external membrane to have greater surface for reactions to occur
113
endosymbiosis
contact between an anaerobic eukaryotic cell comes in contact with an aerobic prokaryotic cell
114
cytosol
gel-like fluid
contains:
- fibres
- enzymes
- inclusion bodies
- droplets
function is to synthesize most proteins in cytosolic ribosomes
115
secretory pathway
route followed by proteins through the ER, the Golgi, the secretory vesicles and lysosomes
116
glycosilation
gluons are hydrophilic and prevent aggregation in folding and are essential in quality control
increase specificity
protect the cells from modifying chemical agents
allows interactions between proteins or cells
essential in sorting
117
ERGIC
complex made of recycled vesicles that move between ER and Golgi
ERGIC 53 or LMAN1 is a cargo receptor that recognizes some glycosilated proteins to bring them to Golgi
118
major cargos
factor 5 or factor 8 of coagulation cascade
if ERGIC 53 is missing, mild coagulation pathology can arise
119
bulk flow
proteins can randomly be incorporated into a vesicle thanks to sucking force that occurs when vesicle forms
120
how are enzymes kept in ER?
enzymes work together in supramolecular complexes
- so they can't be incorporated
