Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

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

lectures 1-9 Flashcards

1
Q

parallel β protein strand

A

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

H bond is angled

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

anti-parallel β protein strand

A

1 AA H-bond to 1 AA in adjacent strand

straight H-bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

reverse/β turn

A

chain sharply reverses direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

loops

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

side chains in tertiary structure interact mostly by ___________ bonds

A

non-covalent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

motifs

A

combination of 2ndary structure elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

ββ motif

A

anti-parallel β strands

H bonded together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

βαβ motif

A

parallel

loop between β and α

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

helix-turn-helix

A

turn between helices

interactions between side chains between α helices

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

leucine zipper

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

tetramer

A

4 chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

collagen

A

3 tight winding chains

collagen helix not alpha helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

mercapto group

A

HS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

nucleation/hydrophobic collapse

A

hydrophobic regions condense/come together

short stretches of 2ndary structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

aggregation

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

compaction

A

tertiary structure forms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

chaperonins

A

assist folding
double donut
7 ATP hydrolysed
proteins can fold without risk of aggregation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

protein disulfide isomerase

A

catalyse oxidation and isomerisation and formation of disulfide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

O2 has low ________

and only ____ is ________

A

solubility

5% dissolved in solution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

1 torr

A

0.13 kPa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

partial pressure of O2 (pO2) in lungs

A

100 torr

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

partial pressure of O2 (pO2) in tissues

A

20 torr

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

muscles are big users of O2 so……..

and…….

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

myoglobin

A 
very high affinity
50% saturation level = 2 torr
simple binding with equilibrium
hyperbolic shaped curve - binding curve
useless as transport protein
only in muscles
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

50% saturation level (P50)

A

how much oxygen present when half of the protein is in oxygen bound form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

haemoglobin

A

sigmoidal binding curve
not simple binding
give O2 to myoglobin at 20 torr in tissues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

prosthetic group

A

cofactor permanently bound by covalent bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

apoprotein

A

without its prosthetic group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

cooperative/allosteric binding

A

4 binding sites collaborate (only in quaternary structure)
not simple binding
sigmoidal curve
2 conformations: T and R state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

T state

A

tense
low affinity
deoxy-Hb

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

R state

A

relaxed
high affinity
Oxy-Hb

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

concerted model of cooperative binding

A

T and R coexist and O2 binding shifts equilibrium

once 1st bound, more likely to shift to R

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

sequential model of cooperative binding

A

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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

describe what occurs when the first O2 binds to Hb

to summarise….

A 
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

2, 3-bisphosphoglycerate (BPG)

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

fetal Hb

A

α₂γ₂

reduced affinity for BPG so increased affinity for O₂

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Bohr effect

A

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
Q

allosteric effectors

A

affect and bind somewhere other than the binding site

47
Q

O₂ is a _____________ of other 0₂ binding sites

A

allosteric regulator

48
Q

3 lipids in membranes

A

phospholipids
glycolipids
cholesterol

49
Q

eicosanoids

A

short range
pain
inflammation

50
Q

key functions of lipids

A

fuel for metabolism
membranes
signalling
vitamins

51
Q

amphipathic

A

both hydrophobic and hydrophilic

52
Q

liposome

A

form bilayer ball

watery inside and outside

53
Q

the membrane is ______________ meaning it closes up again if disrupted

A

self-sealing

54
Q

flippase

A

proteins that flip phospholipids so on side where should be

55
Q

phospholipid structure

A

like triglyceride but 1 fatty acid replaced with phosphate group

glycerol, 2 fatty acids, phosphate

56
Q

sphingolipid structure

A

like phospholipid but 1 FA replaced by hydrocarbon chain that’s part of the sphingosine (not glycerol)

sphingosine + hydrocarbon chain, FA, phosphate

57
Q

carboxylic acid group

A

-COOH

58
Q

what bond is between a glycerol and a fatty acid

A

ester bond

59
Q

saturated fatty acids

A

no DB
increased length=increased melting point
mostly even number of carbons

60
Q

unsaturated fatty acids

A

DB in cis/trans configuration (mostly cis)
trans=straight
cis=more of a kink

more double bonds means lower melting point

61
Q

sphingomyelin structure

A

amino group instead of OH
amide bond not ester
important in myelin sheath

62
Q

glycolipids

A

sphingosine, fatty acid, sugar (instead of phosphate)

63
Q

cholesterol

A 
sterol = modified steroid
4 rings
planar
only in animals
in membranes
basis for sex hormones
rings are rigid, tail is floppy = regulates fluidity
64
Q

melting point Tm

A

transition from solid to fluid like state of membrane

melting point of individual fatty acids contribute to melting point of whole membrane

65
Q

which part of the cholesterol molecule sticks out into water?
and what does this resemble?

A

hydroxyl (OH)

hydrophilic head

66
Q

how does cholesterol buffer fluidity?

A

stiff ring restrains movement at high temps

prevents close packing at low temps

67
Q

how does bacteria regulate fluidity?

A

doesn’t have cholesterol so changes lipid composition

68
Q

fluorescence recovery after photobleaching

A

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
Q

integral membrane proteins

examples

A

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
Q

membrane topology

A

arrangement relative to membrane
doesn’t change
maintained by hydrophobic and electrostatic interactions

71
Q

peripheral membrane proteins

A

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
Q

palmitoylation

A

lipid anchor

hydrophobic anchor onto protein so anchors onto membrane

73
Q

spectrin

A

cytoskeletal protein underneath the membrane
scafolding
keeps in place
needs Ankyrin
binds onto membrane
link between spectrin and integral membrane proteins

74
Q

carbohydrate functions on membranes

A

cell-cell recognition
communication
adhesion
distinguish self/non-self

75
Q

what can cross the lipid bilayer?

what can’t?

A 
small hydrophobic molecules
small uncharged polar molecules
some water (but usually can't)

large uncharged polar
charged ions
charged polar

76
Q

rate of transport across membrane depends on what?

A

size and hydrophobicity

conc. gradient

77
Q

dynamic equilibrium

A

same conc. on both sides of membrane
no net transport
equally move in both directions

78
Q

how do channels open?

A

they are gated

79
Q

uniport transport
symport
antiport

A

single molecule through (passive)

both molecules out same way, co-transport (active)

molecules in opposite directions (active)

80
Q

primary active transport

A

pumps

directly hydrolyse ATP

81
Q

secondary active transport

A

symports/antiports

transport down conc. gradient releases energy which is used for transport against the concentration gradient

82
Q

facilitated diffusion

A

channel or carrier
down conc. gradient
no energy

83
Q

facilitated diffusion is ……………………. than simple diffusion
and….

A

faster
more saturable
more specific

reaches max velocity quicker

84
Q

max velocity Km

lower Km means..

A

quickest rate
saturation level
shows specificity

better affinity for particular molecule

85
Q

3 classes of primary active transporters

A

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
Q

secondary active transporters

A

use co-transport

energy from transport down conc. gradient used to pump against conc. gradient

87
Q

3 methods of active transport

A

ATP-driven pumps
light-driven
coupled transporters

88
Q

sodium potassium pump

A

P-pump
ATPase
3 Na out, 2 K in
ATP hydrolysis , conformational change

89
Q

aquaporins

A

6 transmembrane α-helices
10 different ones in our genome
passive with conc. gradient (osmotic pressure)

90
Q

why does glucose have to go through the cell and can’t go around it?

A

tight junctions between cells

91
Q

what kind of bond is between the base and sugar of nucleotides?

A

glycosidic

92
Q

aldehyde

A

double bonded O

CH=O

93
Q

aldose

A

monosaccharide with 1 aldehyde

94
Q

how does the glucose ring structure form?

A

OH on C-5 bonds to C1

95
Q

isomers

conformations

A

different arrangements

from bond rotations

96
Q

H bond donor

A

polar covalent bond between H and N/O

97
Q

H bond acceptor

A

O/N with lone pairs

98
Q

salt bridges

A

opposite charges interact
H bond and ionic bonds
no transfer of electrons, just charged interactions

99
Q

van der waal’s

A

temporary dipoles induced by proximity

100
Q

ice can made 4 H bonds because..

water is more dense because..

A

2 lone pairs act as acceptors
and 2 Hs as donors

it doesn’t make all 4 H bonds so closer together

101
Q

pH =

A

pKa + log (A/HA)

henderson-hasselbalch

102
Q

Ka =

A

(H)(A) / HA

103
Q

amide bond

A

peptide bond

104
Q

x-ray crystallography
NMR spectroscopy
electron microscopy

A

diffraction

resonance

105
Q

resonance

A

double bond switches from N to O from carbon

106
Q

psi

A

between alpha carbon and carbonyl

107
Q

phi

A

NH3 to alpha C

108
Q

Ramachandran plot

A

psi against phi

determine alpha/beta structure

109
Q

rise

A

1.5A per residue

110
Q

how many residues in every helix turn?

A

3.6

1st year: MCO (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions