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1st year: MCO > lectures 1-9 > Flashcards

lectures 1-9 Flashcards

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1
Q

parallel β protein strand

A

1 AA H-bond to 2 diff AAs in adjacent strand

H bond is angled

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2
Q

anti-parallel β protein strand

A

1 AA H-bond to 1 AA in adjacent strand

straight H-bond

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3
Q

reverse/β turn

A

chain sharply reverses direction

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4
Q

loops

A

longer than turns
chain reverse
no regular structure
in between different β strands

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5
Q

side chains in tertiary structure interact mostly by ___________ bonds

A

non-covalent

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6
Q

bonds in tertiary structure

A

salt bridges
H bond
hydrophobic interaction
disulfide (the only covalent 1, only extracellular)
van der waal’s (tight packing, no holes in proteins)

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7
Q

motifs

A

combination of 2ndary structure elements

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8
Q

ββ motif

A

anti-parallel β strands

H bonded together

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9
Q

βαβ motif

A

parallel

loop between β and α

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10
Q

helix-turn-helix

A

turn between helices

interactions between side chains between α helices

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11
Q

zinc finger motif for DNA binding

A 
α helix and antiparallel β strands
stabilised by zinc ion
in major groove of DNA
transcription factors
dipole ion interactions
salt bridges
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12
Q

leucine zipper

A

long α-helices
in major groove of DNA
leucines between helices interact to hold together
hydrophobic interactions

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13
Q

EF hand, calcium binding motif

A

variation on helix-turn-helix
negative side chains in loop
positive calcium ion in loop by salt bridge
change protein structure depending on if calcium bound or not
not bound = helices move closer
calcium conc. induces conformational change so change activity of protein

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14
Q

domains

A

compact regions may be connected by flexible segment of polypeptide chain
motifs make up domains
fold independently on their own
more difficult to degrade if multi-domains

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15
Q

tetramer

A

4 chains

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16
Q

collagen

A

3 tight winding chains

collagen helix not alpha helix

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17
Q

Anfinsen’s experiment

A

add urea (disrupt H bond,so hydrophobic interactions, and unfolds) and β-mercaptoethanol (reduce disulfide bonds) to RNase
removed chemicals by dialysis
protein refolds
so info for specifying structure is in primary structure (AA sequence)

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18
Q

mercapto group

A

HS

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19
Q

protein folding isn’t random because…

A

2 torsion angles means 3 possible conformations of each angle and so too many possibilities for 1ms folding
can’t go through every possibility, so not random

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20
Q

nucleation/hydrophobic collapse

A

hydrophobic regions condense/come together

short stretches of 2ndary structure

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21
Q

aggregation

A

motifs, domains, molten globule, semi-fluid
not tightly packed, extensive 2ndary structure
no tertiary structure
proteins clump together

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22
Q

compaction

A

tertiary structure forms

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23
Q

in low protein conc………………..

in high………………….

A

folding is favoured

aggregate (so not fold) because might form hydrophobic interactions with other chains and not itself, clump because sticky from hydrophobic surfaces when unfolded

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24
Q

chaperones

A

assist folding
prevent aggregation
bind to unfolded proteins so reduce risk of coming together with other proteins
requires energy because conformational change by ATP hydrolysis

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25
chaperonins
assist folding double donut 7 ATP hydrolysed proteins can fold without risk of aggregation
26
protein disulfide isomerase
catalyse oxidation and isomerisation and formation of disulfide bonds
27
O2 has low ________ | and only ____ is ________
solubility 5% dissolved in solution
28
1 torr
0.13 kPa
29
partial pressure of O2 (pO2) in lungs
100 torr
30
partial pressure of O2 (pO2) in tissues
20 torr
31
muscles are big users of O2 so........ | and.......
need further protein that hold oxygen at 20 torr and release at very low conc. this protein is myoglobin - stores oxygen for tissues when needed
32
myoglobin
``` very high affinity 50% saturation level = 2 torr simple binding with equilibrium hyperbolic shaped curve - binding curve useless as transport protein only in muscles ```
33
50% saturation level (P50)
how much oxygen present when half of the protein is in oxygen bound form
34
haemoglobin
sigmoidal binding curve not simple binding give O2 to myoglobin at 20 torr in tissues
35
prosthetic group
cofactor permanently bound by covalent bonds
36
apoprotein
without its prosthetic group
37
cooperative/allosteric binding
4 binding sites collaborate (only in quaternary structure) not simple binding sigmoidal curve 2 conformations: T and R state
38
T state
tense low affinity deoxy-Hb
39
R state
relaxed high affinity Oxy-Hb
40
concerted model of cooperative binding
T and R coexist and O2 binding shifts equilibrium | once 1st bound, more likely to shift to R
41
sequential model of cooperative binding
O2 binding induces shift from T to R binding of O2 changes conformation of subunit from T to R intermediate state when partially converted (increases affinity)
42
describe what occurs when the first O2 binds to Hb to summarise....
``` O2 binds to iron ion pulls haem up so straight line pulls proximal histidine so pulls helix closer to haem this cascades through the subunit changes interfaces between α and β subunits subunits closer in R state ``` the size of the central cavity changes when O2 is bound
43
2, 3-bisphosphoglycerate (BPG)
doesn't fit in central cavity in R state so binds and locks in T state reducing Hb's affinity for oxygen so better at releasing allosteric regulator for Hb
44
fetal Hb
α₂γ₂ | reduced affinity for BPG so increased affinity for O₂
45
Bohr effect
protons from metabolism reduce the pH which protonates histidine salt bridges form and T state stabilised O₂ released CO₂ lowers pH too and binds to Hb so conformatinal change, salt bridges, stabilise T state
46
allosteric effectors
affect and bind somewhere other than the binding site
47
O₂ is a _____________ of other 0₂ binding sites
allosteric regulator
48
3 lipids in membranes
phospholipids glycolipids cholesterol
49
eicosanoids
short range pain inflammation
50
key functions of lipids
fuel for metabolism membranes signalling vitamins
51
amphipathic
both hydrophobic and hydrophilic
52
liposome
form bilayer ball | watery inside and outside
53
the membrane is ______________ meaning it closes up again if disrupted
self-sealing
54
flippase
proteins that flip phospholipids so on side where should be
55
phospholipid structure
like triglyceride but 1 fatty acid replaced with phosphate group glycerol, 2 fatty acids, phosphate
56
sphingolipid structure
like phospholipid but 1 FA replaced by hydrocarbon chain that's part of the sphingosine (not glycerol) sphingosine + hydrocarbon chain, FA, phosphate
57
carboxylic acid group
-COOH
58
what bond is between a glycerol and a fatty acid
ester bond
59
saturated fatty acids
no DB increased length=increased melting point mostly even number of carbons
60
unsaturated fatty acids
DB in cis/trans configuration (mostly cis) trans=straight cis=more of a kink more double bonds means lower melting point
61
sphingomyelin structure
amino group instead of OH amide bond not ester important in myelin sheath
62
glycolipids
sphingosine, fatty acid, sugar (instead of phosphate)
63
cholesterol
``` sterol = modified steroid 4 rings planar only in animals in membranes basis for sex hormones rings are rigid, tail is floppy = regulates fluidity ```
64
melting point Tm
transition from solid to fluid like state of membrane | melting point of individual fatty acids contribute to melting point of whole membrane
65
which part of the cholesterol molecule sticks out into water? and what does this resemble?
hydroxyl (OH) hydrophilic head
66
how does cholesterol buffer fluidity?
stiff ring restrains movement at high temps | prevents close packing at low temps
67
how does bacteria regulate fluidity?
doesn't have cholesterol so changes lipid composition
68
fluorescence recovery after photobleaching
measure lateral diffusion of membrane proteins/lipids label membrane with fluorophores (covalently) laser bleach fluorophores so stop fluorescing measure how quick other fluorophores move into area so diffusion rate
69
integral membrane proteins | examples
traverse all the way through 7 transmembrane proteins have 7 α-helices β-barrel protein: forms pore, H bonds between β sheets, amino acids stick out and interact with lipid bilayer ICAM Bacteriorhodopsin porins
70
membrane topology
arrangement relative to membrane doesn't change maintained by hydrophobic and electrostatic interactions
71
peripheral membrane proteins
interact non-covalently with face/combine to integreal/covalently anchor to membrane from modification of FA palmitoylation electrostatic interactions H bonds van der waals
72
palmitoylation
lipid anchor | hydrophobic anchor onto protein so anchors onto membrane
73
spectrin
cytoskeletal protein underneath the membrane scafolding keeps in place needs Ankyrin binds onto membrane link between spectrin and integral membrane proteins
74
carbohydrate functions on membranes
cell-cell recognition communication adhesion distinguish self/non-self
75
what can cross the lipid bilayer? | what can't?
``` small hydrophobic molecules small uncharged polar molecules some water (but usually can't) ``` large uncharged polar charged ions charged polar
76
rate of transport across membrane depends on what?
size and hydrophobicity | conc. gradient
77
dynamic equilibrium
same conc. on both sides of membrane no net transport equally move in both directions
78
how do channels open?
they are gated
79
uniport transport symport antiport
single molecule through (passive) both molecules out same way, co-transport (active) molecules in opposite directions (active)
80
primary active transport
pumps | directly hydrolyse ATP
81
secondary active transport
symports/antiports | transport down conc. gradient releases energy which is used for transport against the concentration gradient
82
facilitated diffusion
channel or carrier down conc. gradient no energy
83
facilitated diffusion is ......................... than simple diffusion and....
faster more saturable more specific reaches max velocity quicker
84
max velocity Km lower Km means..
quickest rate saturation level shows specificity better affinity for particular molecule
85
3 classes of primary active transporters
P-type pumps - phosphorylate themselves during transportation cycle, so ATP hydrolysed F-type pumps - use proton gradient to synthesise ATP from ADP and Pi ATP binding cassette (ABC) transporter - pumps small molecules instead of ions, hydrolyse ATP
86
secondary active transporters
use co-transport | energy from transport down conc. gradient used to pump against conc. gradient
87
3 methods of active transport
ATP-driven pumps light-driven coupled transporters
88
sodium potassium pump
P-pump ATPase 3 Na out, 2 K in ATP hydrolysis , conformational change
89
aquaporins
6 transmembrane α-helices 10 different ones in our genome passive with conc. gradient (osmotic pressure)
90
why does glucose have to go through the cell and can't go around it?
tight junctions between cells
91
what kind of bond is between the base and sugar of nucleotides?
glycosidic
92
aldehyde
double bonded O | CH=O
93
aldose
monosaccharide with 1 aldehyde
94
how does the glucose ring structure form?
OH on C-5 bonds to C1
95
isomers | conformations
different arrangements | from bond rotations
96
H bond donor
polar covalent bond between H and N/O
97
H bond acceptor
O/N with lone pairs
98
salt bridges
opposite charges interact H bond and ionic bonds no transfer of electrons, just charged interactions
99
van der waal's
temporary dipoles induced by proximity
100
ice can made 4 H bonds because.. | water is more dense because..
2 lone pairs act as acceptors and 2 Hs as donors it doesn't make all 4 H bonds so closer together
101
pH =
pKa + log (A/HA) henderson-hasselbalch
102
Ka =
(H)(A) / HA
103
amide bond
peptide bond
104
x-ray crystallography NMR spectroscopy electron microscopy
diffraction | resonance
105
resonance
double bond switches from N to O from carbon
106
psi
between alpha carbon and carbonyl
107
phi
NH3 to alpha C
108
Ramachandran plot
psi against phi | determine alpha/beta structure
109
rise
1.5A per residue
110
how many residues in every helix turn?
3.6

1st year: MCO (6 decks)

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