MT1 Flashcards
1
Q
nucleic acids
A
make up genetic info and encode proteins
2
Q
lipids
A
energy storing, signaling and structural components of cell membranes
3
Q
carbohydrates
A
energy storing, structural componenets
4
Q
water’s 3 highs
A
high heat capacity -> stable temp to support life
high heat of vaporization -> cool down the body of organisms
higher density than its solid form-> prevents lakes from freezing over
5
Q
water structure
A
bent and polar, 104.5 between the H’s meaning the dipoles can’t cancel (make net dipole!)
O has partial -
6
Q
dipole-dipole int
A
attractive int between 2 permanent dipoles
7
Q
H bonding
A
special dipole-dipole for H atom bonded to only O, N, or F
happens in water is is what causes the 3 highs
bond length is long
weaker than covalent bonds
water can bond with up to 4 neighbors (actually though at rm temp 3.4 other water molecs)
8
Q
ionic interactions
A
ion-ion and ion-dipole
metal ion and anion group
opposite charges (anion wants positive side, cation wants negative of polar molec)
water dissolves because hydration (shell!)
9
Q
van der Waals
A
weakest but more universal intermolecular force
transient, induced dipole-dipole
need close enough proximity, but if too close they become repelled
longer radius than covalent
10
Q
hydrophobic int
A
major driving force for protein folding and cell membrane assembly
entropy! water makes cages around hydrophobic stuff, which also wanna bind so with aggregatopn, more entropy ebcause less ordered water because less esxposed nonpolar surface
11
Q
COO- pKa
A
~2
12
Q
NH3+
A
~10
13
Q
lys pKr
A
10.5
14
Q
arg pKr
A
12.5
15
Q
his pkr
A
6.0
16
Q
asp pkr
A
3.7
17
Q
glu pkr
A
4.3
18
Q
tyr pkr
A
10.1
19
Q
cys pkr
A
8.2
20
Q
size exclusion chromatography
A
small proteins flow through the beads’ channels whereas large flow around the beads (small proteins elute slower)
21
Q
ion exchange chromatography
A
cation: + proteins interact more with a neg matrix > + proteins elute slower
anion: - proteins interact more with a + matric > neg proteins elute slower
22
Q
phosphoylation
A
thr, ser, tyr in eukaryotes; his in bacteria/plants
critical for regulation of enzyme activity, protein protein int, and signal transduction
23
Q
Ubiquitination
A
protein degradation, translation regulation, etc: lys
24
Q
Lipidation
A
(target proteins to membranes): gly, cys
25
Acetylation
(epigentic regulation, histone structure, and int with DNA): lys
26
Carboxylation
(increases affinity for Ca): glu
27
Glycosylation
(protein stability, recognition (40 human diseases are caused my mis-this): ser, thr, asn
28
phi angle
N-Ca
29
psi angle
Ca-COOH bond
30
ramachandran plot
B sheets at top left
L a helix off to the right
R a helic at bottomer area on left
31
glycine rama plot
symmetric, all the way down 2 sides
32
proline rama plot
on the left, down, but smaller than gly
33
pre-proline
also rigid like proline, just not as much so a tad messier
34
a folds
```
helix bundle (like a bundle)
helix-loop-helix (EF hand) (like 2 a helices in an L like formation~)
what do they look like?
```
35
helix bundle
```
4 helices
amphipathic helices
the inward side is hydrophobic
other faces (exposed) are polar/charged
example: human growth hormone
4 a helices with each other
```
36
B folds
```
beta barrel (cylinder-like)
beta propeller (propeller shape)
```
37
B barrel
formed from antiparallel beta sheets
lots of sizes and topologies, neighboring strands are often not adjacent in aa seq
strandds tilted 40 degrees to the barrel axis
fns: nutrient transport, signaling, motility, and survival
eg. retinol binding protein: vit A is hydrophobic so needs help to move through blood stream, and B barrel is that, can hold it inside!
38
alpha helix
spiral structure of polypep with 3.6 residues/turn and 5.4 rise/turn
side chains point out
helical turns held by 3-4 H bonds (from the cOoh and the nH)
macro dipole because all pep have dipoles with similar orientation
amino always + and carboxyl always -
can be right/left handed (use your hand and the whichever matched the curve is the anser) (proteins mostly R) (R is most stable for L aa)
ala very likely to be a helix
gly no (too flexible) and pro no (not flexible)
stability affect by: interactions between R groups, steric hindrance, pro/gly, end int
39
beta strand
zig-zag shape, alt side chains point in opp dir, 2/more segments of poly-pep run alongside each other
nearby are either // or anti//
B sheet stabilized by inter-strand H bonds
anti//: same side spacing of side chains is 7, perpendicular to strands are teh H bonds, aa forms 2 H boonds with another aa on neighbor strands
//" same side spacing of side chains is 6.5, H bonds are angled, less stable, aa forms 2 H boonds with another aa on neighbor strands
40
a/B fold
a/B horseshoe (horseshoe shape) (leu repeaters)
a/B Rossmann fold (pyramid~like)
a/B barrel (circuclar)
41
a/B barrels
donut shape w/ // B strands inner and a helices outer, alternation of a and B
example: TIM (triosephosphate isomerase)
essential in glycolysis and efficient energy production, said to be cat perfect, billion times faster rxn
42
a + B fold
have both a and B but don't alt regularly
mostly anti// B strands
less common than a/B
eg. GFP: anti// B barrel with a helices in the cilinder lumen, need for fluorescent proteins and therefore seeing for science!
43
solubilize or stabilize hydrophob functional groups or proteins
B barrels
44
Contains enzyme active sites
Beta-propeller neuraminidase
| TIM barrel
45
recognize/bind specific ligands
EF hand motif for binding calcium
Horseshoe (leu-rich) repeats for microbes specific molecs
SH2 motif for binding phosphotyrosines
46
primary structures
held by covalent pep bonds
47
secondary structures
local folding of polypep driven by H bonds
48
tertiary structures
distant int between groups of single protein driven by hydrophob int and covalent disulfide bonding, recognizable folds (super 2nd): all motifs
49
Quarternary structures
completed overal struct of fun protein via int between diff subunits (polypep)
50
Fibrous proteins
long fiber/sheet
structural purpose
repetitive AA seq
primarily a single type (2nd struct)
less sensitive to changes in pH, temp, etc
eg. keratin, collagen, fibroin, elastin, etc
generally insoluble in water
51
globular proteins
globular shape (spherical)
functional purpose (binding ligands, enzymes, etc)
irregular aa seq
often multiple types of 2nd structures
more sensitive to changes in pH, temp, etc
eg. hemoglobin, insulin, immunoglobin
generally soluble in water
52
a-keratin
lots of disulfide bonds stabilize protofilament and filament bundles
super-bundle of coiled coil
2 long a helices twist to form a coiled coil
2 coiled coils are arranged in a staggered fashion in protofilaments
2 protofilaments are staggers to make the protofibril
4 protofibrils twist in right handed form to make intermed filament
53
collagen
most abundant protein in animals
main structural component of our connective tissue (bones, skin, eyes, tendons)
some are stronger than steel
aging>body produces less collagen>wrinkles and join weaken
rich in gly and pro
3 L helices, Gly-X(proline)-Y(hydroxyl proline)
3.3 residues/turn, but looser than right handed a-helix
makes triple helix to form collagen fibers
make filaments (stabilized by H bonds between gly H and P carboxyl C)
54
fibroin
major in silk and spider webs
| made of anti// B sheets rich in ala/ser and gly (allow for tight packing so ^ tensile strength)
55
coiled coil
usually 2 a helices, twist together, interact e/ each other thru side chain int (hydrophob and elecstatic)
hepta repeat patter of Leu
(3.5 aa/turn)
also often called leucine zipper
56
Anfinsen's experiment
tested ribonuclease A by:
denaturation with urea and B-mercaptoethanol
then renaturation through dialysis (removes the stuff from the protein with a dialysis membrane (makes it equib))
it refolded then> shows that an aa seq of a polypep contains all info needed to fold chain to native structure
57
Levinthal's paradox
there are too many possibilities for the folding to be random, it would take longer than the universe has been alive
58
thermodynamics of protein folding
unfolded: fewer covalent int, higher enthalpy, lower entropy
folded: more non-covalent int, lower enthalpy, greater entropy
59
protein denaturation: heating:
(adding energy) causes the atoms to vibrate so rapidly and violently that the bonds are disrupted (affects primarily H bonding)
60
protein denaturation: pH variation
alters ionization of aa side chains which alters charge distribution (affects H bonding and ionic int)
61
protein denaturation: detergents:
(amphipathic molecs) assosicated with nonpolar residues and disrupt the hydrophob int
62
protein denaturation: chaotropic agents
(urea, guanidinium) ions/small org molecs that at high []s (5-10M) disrupt H bonding
63
protein denaturation: reducing agents
(B-Mercaptoethanol) disrupting disulfide bonds and tertiary structures
64
molten globules
folding intermediate
energy higher than native state, but lower than unfolded
unfolded>MB is fast>folded is slow
contain 2ndary struct, it's reaaal, liquid like core
65
folding funnels
if wide and smooth> multiple folding pathways but no stable intermeds
if bumpity> multiple folding paths and several semi-stable intermeds
if flat and a drop> few folding possibility and no stable folding intermeds
if one giant hump>single stable folding intermed motif en route to natively folded protein
66
protein disulfide isomerases (PDIs)
folding assistant enzymes
corrects non-native disulfide binds because of oxidative stress
oxidative: form S-S bonds by exchanging own disulfide bond with substrate
reduced: correct the incorrect S-S bonds in misfolded protein
structure: 4 domains, U shape, a and a' cat (cys) and b and b' non cat bind with hydrophob int
B has low affinity biting sites so broad specificity
67
chaperones
folding assistant enzymes, fixing aggregation, due to exposed hydrophobic patches of folding intermediates
68
mechs to deal with already misfolded proteins
disaggregated: degraded by 26S proteasome
if not possible (terminal or too big): disposed of by autophagy
if not that: accumulate in the ER (ER stress), it induces unfolded protein response
69
26S proteasome
```
made up of:
19S regulatory partical: cap pfor 20S, binds to ub substates and cleave ub off to reuse
unfold with ATP and pass to 20S
20S core protease: cyclinder of a and B
helps with catalysis, no ATP
```
70
autophagy
promote recycling and salvage of cellular nutrients, enabling cell survival during starvation, helps in protein homeostasis and quality control (with proteasomes)
programmed cell death during development/pathogen infection
macro-
micro-
chaperone mediated -
71
ER and ER stress
```
protein folding (secreted and surface proteins), lipid synthesis, and Ca2+ storage
UPR induction> activate sensors tht make transcrip factors for activating genes to ^ protein folding capacity, down load of those entering too, feedback loops
```
72
aggregation of misfolded proteins
exposed hydrophobic patches, can lead to toxicity and stuff
mutations and environmental factors
amyloid fibers
they can caused it
73
AT h bonds
2
74
GC h bonds
3
75
DNA structure
right hand double helix, with major and minor grooves
ribose and phosphate are outside the helix
hydrophobic bases are inward but accessible through grooves
adj bases are 3.4 A apart
36A l in turn, with 10.5 base pairs
76
B-DNA
most common
right handed
10.5bp/turn, 36A in turn
width of dsDNA 20A
77
A-DNA
shorter helix
dehydrated dsDNA
right handed helices
1 turn=28A
78
Z-DNA
longer helix
left handed helices
major grooves de-emphasized
occurs occasionally in short stretches of DNA: local deformation affects protein binding and hence regulate gene expression
79
hairpin
palindromic repeat on one side
80
cruciform
palindromic and on both strands
81
triple helix
one strand had a long stretch of only pyrimidines or purines
| more stable at lower pH>TAT or CGC
82
quadraplex
4 guanosine residues, only in very rich C DNA, stable under variety of conditions
strands can be // of anti//
occurs in vivo telomeres
83
Bases?
other flashcards
84
tRNA 2ndary struct
4 complimentary regions, 4 loops, anticodon base pairs with mRNA
85
RNA tertiary struct
due to enormous rotational freedom in backbond of it's non-base-paired regions, are unique, critical for fun 3D struct
depends on cations because phosphate has neg charge and repel so cations shield and stabilize
86
tert things
tRNA
natural biosensors (riboswitch)
enzymes (ribozymes)
87
tRNA
has L shape
D and T loop align
folded through co-axial stacking of adj stems
88
riboswitch
used by bacteria to sense metabolites
1. aptamer domain binds the ligand
2. switching seq: changes 2ndary struct upon ligand binding (spants regions of aptamer and expression plat)
3. expression platform: protein-encoding domain
(causes translation to abort if metabolite binds)
89
helix-turn-helix
lamda phage Cro and related repressors
tryptophan repressor
lac repressor
90
beta-sheet saddle
TATA box binding protein
91
homeobox
antennapedia
92
anti// beta barrel
p53
93
zinc finger
Zif 268
| steroid receptors
94
zinc finger
```
Zif 268
steroid receptors
zinc coordinated by His and Cys residues
helic makes specific contact with DNA
proteins often contain more than one zinc fingers (Zif has 3, and steroid has 2)
not always binding DNA
```
95
leucine zippers (bZIP)
GCN4
homo or heterodimers
form a coiled coil with heptad repeat, no S-S bonds
DNA binding domain contacts successive major grooves with basic residues on opposite sides of the helix
96
lamda repressor
```
road block for RNA poly
HTH
contact DNA with helix 3
bind successive major grooves
bind palindromic seq
form homodimers
activates lysogenic cycle
dimerizes via a helices
```
97
tryptophan repressor
```
road blocks for RNA poly
allosterically regulated by metabolites
HTH
bind major grooves
bind DNA in presence of Trp
Trp binding triggers its DNA association
controls Trp synthesis
dimer
little change in DNA structure
```
98
lac repressor
```
road blocks for RNA poly
allosterically regulated by metabolites
HTH
bind major grooves
bind DNA in the absence of lactose
lactose binding triggers its DNA dissociation
controls lac metabolism
tetramer
induce a hairpin structure
```
99
TATA box binding protein
ubiquitious in eukaryotes
deforms the DNA
acts as a scaffold for assembly of transcrip machiery
contacts DNA minor groove via beta strans
binds TA rich seq
hydrophob int
100
homeobox
```
like antennapedia
similar to lamda repressor but works as a monomer
helix 3 is the recognition helic
eukaryotic cells
controls developmental patterning
```
101
p53
tumor suppressor...
3 domains (transactivation, binding, and oligomerization)
bind DNA as tetramer
DNA binding domain is a B barrel with 2 helices
stabilized by zinc
contacts DNA via helix and loops
arg: causes loss of contact with DNA and loss of stability (dealing with sugar and zinc respectively) and issue with seq-specific bidning of nuc in major groove
