lectures 1-9 Flashcards
parallel β protein strand
1 AA H-bond to 2 diff AAs in adjacent strand
H bond is angled
anti-parallel β protein strand
1 AA H-bond to 1 AA in adjacent strand
straight H-bond
reverse/β turn
chain sharply reverses direction
loops
longer than turns
chain reverse
no regular structure
in between different β strands
side chains in tertiary structure interact mostly by ___________ bonds
non-covalent
bonds in tertiary structure
salt bridges
H bond
hydrophobic interaction
disulfide (the only covalent 1, only extracellular)
van der waal’s (tight packing, no holes in proteins)
motifs
combination of 2ndary structure elements
ββ motif
anti-parallel β strands
H bonded together
βαβ motif
parallel
loop between β and α
helix-turn-helix
turn between helices
interactions between side chains between α helices
zinc finger motif for DNA binding
α helix and antiparallel β strands stabilised by zinc ion in major groove of DNA transcription factors dipole ion interactions salt bridges
leucine zipper
long α-helices
in major groove of DNA
leucines between helices interact to hold together
hydrophobic interactions
EF hand, calcium binding motif
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
domains
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
tetramer
4 chains
collagen
3 tight winding chains
collagen helix not alpha helix
Anfinsen’s experiment
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)
mercapto group
HS
protein folding isn’t random because…
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
nucleation/hydrophobic collapse
hydrophobic regions condense/come together
short stretches of 2ndary structure
aggregation
motifs, domains, molten globule, semi-fluid
not tightly packed, extensive 2ndary structure
no tertiary structure
proteins clump together
compaction
tertiary structure forms
in low protein conc………………..
in high………………….
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
chaperones
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
chaperonins
assist folding
double donut
7 ATP hydrolysed
proteins can fold without risk of aggregation
protein disulfide isomerase
catalyse oxidation and isomerisation and formation of disulfide bonds
O2 has low ________
and only ____ is ________
solubility
5% dissolved in solution
1 torr
0.13 kPa
partial pressure of O2 (pO2) in lungs
100 torr
partial pressure of O2 (pO2) in tissues
20 torr
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
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
50% saturation level (P50)
how much oxygen present when half of the protein is in oxygen bound form
haemoglobin
sigmoidal binding curve
not simple binding
give O2 to myoglobin at 20 torr in tissues
prosthetic group
cofactor permanently bound by covalent bonds
apoprotein
without its prosthetic group
cooperative/allosteric binding
4 binding sites collaborate (only in quaternary structure)
not simple binding
sigmoidal curve
2 conformations: T and R state
T state
tense
low affinity
deoxy-Hb
R state
relaxed
high affinity
Oxy-Hb
concerted model of cooperative binding
T and R coexist and O2 binding shifts equilibrium
once 1st bound, more likely to shift to R
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)
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
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
fetal Hb
α₂γ₂
reduced affinity for BPG so increased affinity for O₂
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
allosteric effectors
affect and bind somewhere other than the binding site
O₂ is a _____________ of other 0₂ binding sites
allosteric regulator
3 lipids in membranes
phospholipids
glycolipids
cholesterol
eicosanoids
short range
pain
inflammation
key functions of lipids
fuel for metabolism
membranes
signalling
vitamins
amphipathic
both hydrophobic and hydrophilic
liposome
form bilayer ball
watery inside and outside
the membrane is ______________ meaning it closes up again if disrupted
self-sealing
flippase
proteins that flip phospholipids so on side where should be
phospholipid structure
like triglyceride but 1 fatty acid replaced with phosphate group
glycerol, 2 fatty acids, phosphate
sphingolipid structure
like phospholipid but 1 FA replaced by hydrocarbon chain that’s part of the sphingosine (not glycerol)
sphingosine + hydrocarbon chain, FA, phosphate
carboxylic acid group
-COOH
what bond is between a glycerol and a fatty acid
ester bond
saturated fatty acids
no DB
increased length=increased melting point
mostly even number of carbons
unsaturated fatty acids
DB in cis/trans configuration (mostly cis)
trans=straight
cis=more of a kink
more double bonds means lower melting point
sphingomyelin structure
amino group instead of OH
amide bond not ester
important in myelin sheath
glycolipids
sphingosine, fatty acid, sugar (instead of phosphate)
cholesterol
sterol = modified steroid 4 rings planar only in animals in membranes basis for sex hormones rings are rigid, tail is floppy = regulates fluidity
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
which part of the cholesterol molecule sticks out into water?
and what does this resemble?
hydroxyl (OH)
hydrophilic head
how does cholesterol buffer fluidity?
stiff ring restrains movement at high temps
prevents close packing at low temps
how does bacteria regulate fluidity?
doesn’t have cholesterol so changes lipid composition
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
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
membrane topology
arrangement relative to membrane
doesn’t change
maintained by hydrophobic and electrostatic interactions
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
palmitoylation
lipid anchor
hydrophobic anchor onto protein so anchors onto membrane
spectrin
cytoskeletal protein underneath the membrane
scafolding
keeps in place
needs Ankyrin
binds onto membrane
link between spectrin and integral membrane proteins
carbohydrate functions on membranes
cell-cell recognition
communication
adhesion
distinguish self/non-self
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
rate of transport across membrane depends on what?
size and hydrophobicity
conc. gradient
dynamic equilibrium
same conc. on both sides of membrane
no net transport
equally move in both directions
how do channels open?
they are gated
uniport transport
symport
antiport
single molecule through (passive)
both molecules out same way, co-transport (active)
molecules in opposite directions (active)
primary active transport
pumps
directly hydrolyse ATP
secondary active transport
symports/antiports
transport down conc. gradient releases energy which is used for transport against the concentration gradient
facilitated diffusion
channel or carrier
down conc. gradient
no energy
facilitated diffusion is ……………………. than simple diffusion
and….
faster
more saturable
more specific
reaches max velocity quicker
max velocity Km
lower Km means..
quickest rate
saturation level
shows specificity
better affinity for particular molecule
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
secondary active transporters
use co-transport
energy from transport down conc. gradient used to pump against conc. gradient
3 methods of active transport
ATP-driven pumps
light-driven
coupled transporters
sodium potassium pump
P-pump
ATPase
3 Na out, 2 K in
ATP hydrolysis , conformational change
aquaporins
6 transmembrane α-helices
10 different ones in our genome
passive with conc. gradient (osmotic pressure)
why does glucose have to go through the cell and can’t go around it?
tight junctions between cells
what kind of bond is between the base and sugar of nucleotides?
glycosidic
aldehyde
double bonded O
CH=O
aldose
monosaccharide with 1 aldehyde
how does the glucose ring structure form?
OH on C-5 bonds to C1
isomers
conformations
different arrangements
from bond rotations
H bond donor
polar covalent bond between H and N/O
H bond acceptor
O/N with lone pairs
salt bridges
opposite charges interact
H bond and ionic bonds
no transfer of electrons, just charged interactions
van der waal’s
temporary dipoles induced by proximity
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
pH =
pKa + log (A/HA)
henderson-hasselbalch
Ka =
(H)(A) / HA
amide bond
peptide bond
x-ray crystallography
NMR spectroscopy
electron microscopy
diffraction
resonance
resonance
double bond switches from N to O from carbon
psi
between alpha carbon and carbonyl
phi
NH3 to alpha C
Ramachandran plot
psi against phi
determine alpha/beta structure
rise
1.5A per residue
how many residues in every helix turn?
3.6
