Final Flashcards
(673 cards)
1
Q
what are the fundamental units of life
A
cells
2
Q
what do cells use overall in organisms
A
relatively small set of carbon based metabolites to create polymeric machines, suprmolecular structures and information repositories
3
Q
what state do living organisms exist in
A
dynamic steady state, never at equilibrium with their surroundings
4
Q
why cant organisms be in equilibirum with their surroundings
A
we would be dead
5
Q
what do cells have the capacity for
A
precise self replication and self assembly using chemical information stored in gemoe
6
Q
do living organisms change overtime
A
yes by gradual evolution
7
Q
size difference of a bacteria cell and an animal cell
A
bacteria is much smaller, animal usually 10x larger
8
Q
Angstrum
A
1 x 10^-10
9
Q
out side difference or similarties of animal and bacteria cell
A
both have plasma membrane
10
Q
inside differences and similarities of animal and plant cell
A
both have cytoplasm
animal cells are membrane bound organelles (bacteria is not)
genetic info held in the nucleus of animals
genetic info floats in bacteria
both have ribosomes responsible for reading mRNA
11
Q
quote about ecoli and elephant
A
what is true of ecoli is true of the elephant
12
Q
the domains of life
A
bacteria, archea, and eukarya
13
Q
what can classify living things
A
their energy and their carbon source
14
Q
what are our main sources of energy
A
organic chemicals
15
Q
what is the light microscope
A
wavelengths of visible length (400-750 nm
you can see the cell with this but cant tell info about the small things inside the cell
16
Q
size of a typical cell
A
10s of um
usually 20um-20,000nm
17
Q
size of plasma membrane
A
50A
18
Q
size of DNA
A
18A
19
Q
size of nucleotides
A
10A
20
Q
size of amino acids
A
3-5A
21
Q
Size of protein
A
5A but could be as large as 10A i things are sticking out
22
Q
size of C-C bond
A
1.5A
23
Q
size of C-H
A
1.1 A
24
Q
what makes up most of the cell
A
water
25
what else makes up a cell
proteins
RNA
polysaccahirdes
lipids
monomeric subunits
DNA
inorganic ions
26
valence electrons in
H
C
N
P
O
S
Halogens
1H
4C
5N
5P
6O
6S
7Halogens
27
LOOK AT FUNCTIONAL GROUPS
FUNCTIONAL GROUPS
28
what are biological molecules combinations of
functional groups
29
what makes up a double bond
sigma bond + pi bond
30
what is the stronger bond in a double bond
pi bond
31
diasteriomer
not a mirror image
32
enantiomer
mirror immage
33
why is metabolic energy spent
to do cellular work
34
how does entropy change in a system
entropy of the system and surroundings increase
35
where is potential energy
nutrients in environemnt (complex molecules like sugars and fats)
sunlight for plants
36
what are the energy transductions that accomplish work
chemical transformations within cells
heat
metabolism
polymerition
37
what are the chemical transformations within cells
cellular work:
chemcial synthesis
mechanical work
osmotic and electrical gradients
light production
genetic information trasnfer
bascially take potential enery and convert it to do work, work will synthesize new molecules
38
does heat cause more or less disorder
more
cells produce lots of excess eat as a side product, keeps our body at a warm temp
disorder goes into environment by heating up
39
what does metabolism do
produces compounds simpler than the initial fuel molecules
breaking down sugars and fats we breathe out small molecules like CO2 which are more disordered
40
what is the polymerization that happens in cells
simple compounds polymerize to form information rich macromolecules, DNA, RNA and protiens
41
what is the main energy currency
ATP
42
how to break ATP
hydrolysis, water across the bond
43
ATP equation
H2O + ATP (4-) --> ADP (3-) + Pi(2-) + H+
44
what happens when you phosphorylate glucose
means you add them together and the sum is favorable
45
anabolic
builds, what it is using
46
catabolic
break down
47
basic idea of metabolism
organisms take in energy and break down into simple molecules
48
what allows for evolution
changes in heredity
49
how much change is needed for a new mutation
1 base change can change the amino acid which changes its function
50
what did life likely evolve from
RNA
51
what do we think ancestral cells did to allow for the genetic diversity we have today
ancestral cell engulfed mitocondria leading to more complex eukaryotic cells
52
what is water
a small bend molecular with polar bonds
53
partial charges on water
partial positives on the 2 hydorgens and partial negatives on the 2 sets of oxygen electrongs
54
what can water molecules do
ionize
55
what does ionization allow for in water
allows protons to hop in aqueous solution,
56
what explains the high ionic mobility of the H+ in solution
ionization
57
pH=
-log[H+]
58
pOH=
-log[OH-]
59
pH+pOH=
14
60
PRACTICE PH AND POH EQUATIONS
EQUATIONS
61
weak acid
acid that doesnt completely dissociate in a solution
62
conjugate base
removal of a proton from an atom
63
monoprotic acid
can only donate one proton
64
monoprotic acid examples
acetic acid and ammoniun ion
65
diprotic acid
have 2 acidic hydrogen atoms, yields 2 hydrogen ions per acid molecule
66
examples of diprotic acids
carbonic acid, bicarbonate, glycine carboxyl, glycine amino
67
triprotic acid
has 3 acidic hydrogen atoms
68
triprotic acid examples
phosphoric acid, dihydirgen phosphate, monohydrogen phosphate
69
what is a buffer
mixture of a weak acid and their conjugate base allowing for pH consistance
70
when do you do a weak acid calculation
when no buffer is present
71
Henderson Hasselbalch equation
pH=pka + log[A-]/[HA]
72
main buffering system in cells
phosphate system
73
main buffering system in blood
bicarbonate system
74
what happens to the buffering system in people with diabetes
body will oxidize fat causing your body to be more acidic
75
Special traits of water
strong intramolecular forces (hydrogen bonds)
High melting and boiling points
high heat of vaporization
76
how many hydrogen bonds can water form
4
77
how many hydrogen bond acceptors in water
2
78
how many hydrogen bond donors in water
2
79
ice water males how many hydirgen bonds
4
80
liquid water makes how many hydrogen bonds
3.4
81
why are the hydrogen bonds in liquid water less than it solid water
the moelcules of water can be closer in liquid form so it increases the density
82
what has a lower density ice or liquid water
ice, why it floats
83
why do snowflakes have hexagonal symmetry
increase in entropy drives the melting of ice and the evaporation of water
84
what are the hydrogen acceptors
O or N or F (rare)
85
hydirgen donors
water
86
characteristic of a hydrogen donor
electronegative atom
87
characterisitic of a hydorgen acceptor
has a lone pair
88
what types of hydrogen bonds are stronger
shorter and straighter ones
89
what is the solubility of salts in water driven by
an increase in entropy
90
what is more soluble in water salts or less polar solvents
salts
91
increase in entropy
disorder
92
what is the physical reason why salt is soluble in water
the water is more ordered but is outcompeted by the sakt
93
what state does oxygen have the most freedom in
gas phase
94
does a high or low temp favor the gas phase of water
high
95
how does the temp of oceans and ponds affect water and oxygen content
high temps favor the gas phase which will decrease the O2 content affecting the wildlife in oceans and ponds
96
hydrophobic
doesnt like water
97
hydrophillic
likes water
98
what type of interactions bind enzyme with substrate
noncovalent
99
when are water molecules displaced
when substrate binds to enzyme
100
are non covalent interactions strong or weak
weak
101
what is osmotic pressure
force necessary to resist water movement, there is a semipermeable barrier that H2O moves through but solvent does not
102
in a more concentrated solution will water move in or out?
in
103
how many amino acids are there
20
104
what joins amino acids together
peptide bonds or amide linkages
105
proteins are separated based on what?
differences in their chemical and functional properties
106
what are the building blocks of proteins
amino acids
107
zwitter ion
in pH range of 3-10, neutral because one is protonated and one is not
108
what orientation are amino acids in nature
L
109
what is the orientation proteins are built
N --> C
110
what is an amino acid residue
lost H2O
111
quality of the peptide backbone
flexible
112
N-Ca bond
Phi
113
Ca-C bond
psi
114
C-N
omega
115
dihedral angle
angle between planes formed by the backbone
116
pKa of the carboxyl end
2
117
pka of amino end
9
118
what is the simplest amino acid
glycine
119
pI
pH when charge on molecule is zero --> in between buffering zones
120
glycine
G
121
alanine
A
122
proline
P
123
valine
V
124
leucine
L
125
isoleucine
I
126
methionine
M
127
Phenylalanine
F
128
Tyrosine
Y
129
Tryptophan
W
130
Serine
S
131
Threonine
T
132
Cysteine
C
133
Asparagine
N
134
Glutamine
Q
135
Lysine
K
136
Histidine
H
137
Arginine
R
138
Aspartate
D
139
Glutamte
E
140
pKa of tyrosine
10.07
141
pKa of cysteine
8.18
142
pKa of lysine
10.53
143
pKa of histidine
6
144
pKa of arginine
12.48
145
pKa of aspartate
3.65
146
pKa of glutamate
4.25
147
negative hydropathy number
rather be in H2O
148
positive hydropathy number
wants to be in hydrophobic area
149
how can amino acids be modified
methylation and acetylated
150
estimate molecular weight of a protein
residues x 110 Da
151
what is used for protein purification
chromatography columns that use an aqueous buffer as the mobile phase
152
what method seperates proteins based on charge
ion exchnage chromatography
153
cation exchange
cations will stick, must stick to something negative
154
anion exchange
anions stick, resin is positice
155
what do you add if cations are stuck to the column
salt
156
what do you do to a protein with lots of positive charge
change pH increase so its no longer negative and wont stick
157
what method seperates protein based on size
size exclusion chromatography
158
how does size exclusion chromatography work
large ones move quick around the porous beads, small ones get stuck in the beads as they move through
159
negative to size exclusion chromatography
it must be run slow, if it runs too fast by adding concentration but that will increase pressure which can crush/break the beads
160
What type of protein separation is based on tags
affinity chromatography
161
common tags in affinity chromatography
GST
His Tag
ATP-binding domaiin
162
how do proteins move in and SDS gel
unfolded proteins, small ones move further and large ones dont move as far
163
how does isoelectric focusing work
inject protein samples with pH gradient, inject the rpteon we are looking for with neutral charge, separate by sizen
164
what is needed for mass spec
small sample sizes
165
solid phase protein synthesis
chemically from c terminus
166
steps for solid phase protein synthesis
1. link first amino acid at c term
2. need a protecting group (so right part of the backbone reacts)
3. F molecule linked to N terminus as protecting group
4. remove protecting group
5. add next amino acid with protecting group
6. remove protecting group
167
[]
always whatever is within these brackets
168
{}
everything but whats in these brackets
169
visual representation of a protein sequence
sequence logo
170
what is the pauling scale
concept of electrons being shared
171
concept of x ray crystallography
forms cyrtials from x rays, best data from this method
172
what is an ideal methods for determining the protein structure of smaller proteins
2D NMR
173
what is a good method for determining protein structure in large proteins
cryo electron microscopy
174
down side to cryo electrong microscopy
poorer resolution, gives rough approximate shape, not exact
175
what types of proteins do not want to form crystals
nonpolar, hydrophobic, membrane proteins
big floppy ones
176
how long does protein NMR take
6 months
177
levels of protein structure
primary, secondary, tertiary, quaternary
178
primary protein strucutre
amino acid residues connected via covalent bonds (peptide bonds) and disulfide bridges
179
secondary protein structure
common protein folding structure held together by hydrogen bonds between backbone functional groups
180
tertiary protein structure
folded 3D structure of single chain, H bonds and other weak interactions between backbone and side chains
181
quaternary structure
final folded structure with multiple chains (if applicable)
182
orientation of a peptide bond in a protein
usually trans, no free rotation
183
alpha helix protein structure level
secondary
184
what is an alpha helix held together by
hydrogen bonds between functional groups on the backbone
185
rise per amino acid
1.5A/amino acid residue
186
what is the orientation of hydrogen bonds in an alpha helix
parallel to the axis of the helix
187
typical length of a hydrogen bond
2.8-3.1 A
188
what is stronger a shorter or a longer hydrogen bond
shrter
189
which residues favor alpha helix formation
ala
arg
leu
glu
meth
iso
190
where do complementary residues sit in an alpha helix
at the i, i+3 or i+4
191
residues that don't fit with an alpha helix
glycine
proline
192
why is glycine bad for an alpha helix
too flexible
193
why is proline bad for for an alpha helix
too rigid
194
what is the N terminus in an aloha helix stabilized by
more negative residues
195
what is the c terminus of an alpha helix stabilized by
more positive residues
196
what level of protein strucutre is a b-sheet
secondary
197
what is the length of a antiparallel beta sheet per amino acid
3.5A
198
what is the length of a parallel beta sheet per amino acid
3.25 A
199
types of hydorgen bonds in an antiparallel b sheet vs a parallel b sheet
parallel has bent hydorgen bodns
antiparallel has stronger more stable hydirgen bonds
200
minimum number of strands for a b sheet
2
201
globular protein
discrete unit mixture of secondary structure
202
fiberous protein
structural role, forms long fibers
203
examples of fibrous proteins
alpha keratin (lots of alpha helices)
silk (beta sheets in layers)
204
do antiparallel sheets have tight or wide turns ?
tight
205
smallest turn for a beta sheet
4 amino acids
206
how is a beta sheet with 4 residues held together
by a hydrogen bond between the 1st and 4th residue
207
type 1 turn of a beta sheet
residue #2 is a proline in cys conformation
208
type 2 turn of a beta sheet
#3 is a glycine which can rotate easily
209
what is more common a type 1 or type 2 turn
type 1
210
what is CD spectroscopy
peptide will absorb left and right plan polarized light different to measure secondary protein structure
211
alpha keratin
2 alpha helices wrapped around each other
very strong
212
examples of alpha keratin
hair, skin, nails, horns, claws, wool
213
what amino acids are found in keratin
ala, val, leu, iso, met, phe, cys
214
which hand is alpha keratin
2 left handed helices wrapped to make it right handed
215
steps for hair straightening
reduce, curl, oxidize
216
how does hair straightening work
chemically reorganize bonds
217
collagen formation
3 left handed helices wrapped togehter to become right handed
218
the amino acids in collagen
gly
pro
1,4 hydroxylproline
219
what is needed to make hydroxyproline
vitamin c
220
where is the proline and hydroxyproline found in collagen
packed on the outside
221
where is the glycine found in collagen
packed into the middle
222
what is a special characteristics of collagen
cross lining cys residues which have more strength
223
what is silk (fibroin) made up of
layers of anti-parallel beta sheets
224
characteristics of silk
not stretchy, soft, smooth, flexivle
225
amino acids in silk
ala
gly
226
what type of linking is there in silk
no cross linking
227
where is myoglobin found and what does it do
in muscles, holds oxygen
228
even if we back all the atoms togehter in myoglobin and similar proteins what percent will be occupied
75%
25% empty space (not enough room to put anything in that space)
229
will beta sheets always be fully flat
never
230
characterisitcs of folded globular proteins
hydrophobic effect favors 2 layers
b and a segemtns are often separate
N-C term folding
no crossover and right handed connection
favors twisted beta sheets
231
motif
repeats over and over again
B-a-B loops
recognizes strucutre with 2 or more secondary strucutre and their connection
232
a/b barrel
alternates back an d forth
233
what does a higher score mean when mapping proteins
disorder
234
domain
recognizable, independently stable
235
fucntions of domains
catalytic or regulatory
236
what does it mean if amino acids are close together in primary sequence
they are also close in 3D space
237
topology diagrams
illustrate the secondary structure and connections, done to scale, nut cant see L vs R or the overall shape
238
what must quaternary strucutre have
multiple chains
239
hemoglobin strucutre
2 alpha chains
2 beta chains
240
homo vs hetero
same peptides vs
different subunits
241
why cant quanternary srucutre be mirror images
bc we dont have D amino acids
242
ways to monitor protein unfolding
CD spectroscopy
Monitoring W flourescence
243
what does it mean to monitor W flouresence
very sensitive to environment, often W inside and not exposed to water which can be seen
244
what happens to an unfolded protein
it will aggregate so it needs proteins to get it back to its shape
245
ways to unfold a protein
heat
adjust pH
add chemcials
246
what does adding heat do to unfold a protein
breaks disulfide linkages adds a reducing agent
247
what chemicals can be added to unfold a protein
urea, guandium, hydrochloride
248
how to monitor protein folding
melting temp
249
what is the protein melting temp
protein has a certain tolerance to temp before it unfolds
250
examples of chaperones that assist in folding
heat shock proteins
251
why do heat shock proteins form
cells stressed by heat and it creates more chaperone prtoeins
252
what can happen when proteins aggregate
can form large fibrils, mainly happens with extracellular proteins
253
how to avoid fibrils from forming
degrade the protein right away by sending it to the proteosome so the protease can chope it up and destory it
254
how many alpha helicies are in myoglobin
8
255
what type of fold forms in myoglobin
globin fold
256
what is deep in the core of myoglobin
heme group
257
what does the heme group in the myoglobin prevent
oxidation of Fe2+ to Fe3+
258
is myoglobin conjugated or unconjugated
conjugated
259
prosthetic group in myoglobin
heme
260
ligand for myoglobin
oxyegn gas, O2
261
what makes up the heme in myoglobin
porphyrin ring and iron
262
where is the iron held in myoglobin
in the perofrin ring
263
how many connection are there to the iron in the heme group
4
264
how many connections does iron like to have
likes to be octahedral so there are 2 open spaces
265
what specifically connects the iron
proximal his residue
266
what can take up the 6th spot in the iron
pick up an O
267
kd
concentration of ligand needed for 50% of binding sites to be occupied
268
units for Kd
molar
269
do we want a higher or lower kd for good binding to protein
lower
270
what affects how well o2 can bind
influence of a protein
271
how much needs to be conserved for it to still share a strucutre fold
only 1/4
272
what does hemoglobin do
oxyegn carrier
273
how much a RBC does hemoglobin take up
34%
274
what states can hemogobin change to
t or r
275
when is the T state preferred
at low Oxygen concentration
276
when is the R state preferred
at high Oxygen concentration
277
which state favors binding oxyegn
R
278
when does hemoglobin switch from R to T states
changes to R in the lungs to T in the tissues
279
hemoglobin is protonated when
at a low pH
280
when protonated what does the His 146 do
Makes a salt bridge to aspardic acid 94
makes an ion pair to Asp94 which stabilizes the T state
281
what does the CO2 do when on hemoglobin
it is carried by it and will covalently attach to the N terminus releasing more H+ ions
282
whcih state likes to drop of oxygen and i what environment
T state likes to drop off oxygen
more acidic = more oxygen delivered
283
what else regulates oxygen binding to hemoglobin
BPG
284
more CO2 means
more O2 needed
285
what is causes by a single amino acid mutation
sickle cell anemia
286
what is the mutation in sickle cell anemia
beta chain has a EV6 mutation
287
what is an EV6 mutation
glutamic acid changes to valine
288
what happens at the EV6 mutation
allows hemoglobin to polarize make longer strands, make RBCs into rough elongated shapes, usually RBCs need o be round so they can travel through veins
289
what can the EV6 be helpful with
provides protection against malaria
290
what is different about the hemoglobin that fetuses make
it is higher affinity for O2 and uses the O2 in moms blood, after birth they turn off fetal version and turn on human version
291
what are most enzymes
proteins
292
what is the main function of enzymes
lower the activation barrier to allow system to come o equilibrium faster
293
what is a spontaneous delta G
negative
294
what do activation barriers do
slow down a reaction
295
at what temps do enzymes typically function
low temps around 37 degrees C
296
how fast do enzymes work
on the order of us
297
do enzymes produce a lot of side products
no very few
298
what are enzyme cofactors
usually ions, not an amino acid residue but involved in function of enzyme
299
similar to enzyme cofactors
coenzyme
300
what is a coenzyme
not an ion so some small organic molecule involved in function of an enzyme
301
what do enzymes do to lower the activation barrier
speed up the rx. 10^5-10^7x
302
what do covalent bonds in enzymes do
transient so they are temporary bonds that provide an alternative, lower energy reaction pathway
303
what does acid base-catalysis mean
acid donates H+, base accepts H+
304
what do noncovalent interactions in enzymes do
form an ES complex, has weak interactions between enzyme and substrate to stabilize the transition state
305
do enzymes higher or lower substrate entropy
lowers it, holds it steady, makes it more ordered so it can react
306
what is substrate desolvation
when enzymes remove H2O from around the substrate to make available all functional groups of the moelcule
307
how do enzymes help specifically with induced fit
enzyme active sites are complementary to transtion states
308
what shape does the enzyme take
shape that the transition state needs to be
309
which step is an energy diagram is the rate limiting step
biggest one
310
how much does an enzyme bend at the transition state
bends an ideal amount where it cant bend anymore so it snaps
311
what can transition state analogs be
inhibitors
312
how does the inhibitor work for the transition state
looks similar to the transition state but will stop it from occurring
313
what is entropy based rate enhancement
when substrate binds to enzyme they can induce the effects illustrated by this data, by reducing entropy a reaction can happen faster
314
what is rate of the rxn a function of
substrate concentration
315
with more substrate present what does that mean for product
more product that can be formed
316
when does the grpah of product vs time begin to flatten
when we run out of substrate
317
what is the shape of a product vs time graph
rectangular hyperbola
318
what is Km
concentration of substrate at 1/2 max rate of reaction
319
Km<<[S]
Vo=Vmax
320
Km>>[S]
Vo=Vmax[S]/Km
321
what type of line is formed by Vo=Vmax[S]/Km
linear
322
type of line formed by Vo=Vmax
rectangular hyperbola
323
slope of a LB plot
slope=Km/Vmax
324
y intercept of a LB plot
y intercept = 1/vmax
325
X intercept of LB plot
x intercept = -1/Km
326
what is the best data for a perfect enzyme
10^9
327
why can't an enzyme go faster than 10^9
bc of diffusion, 10^9 is the diffusion control limit
328
units of Kcat
s^-1
329
units of Km
molar
330
units of Kcat/Km
M^-1s^-1
331
what does not change in competitive inhibition
Vmax
332
what is competitive inhibition
Inhibitor takes up the S spot, get enzyme inhibitor complex
333
graph of competitive inhibitoion
lines over lap
334
do good inhibitors have big or small Kis
small
335
what shows the influence of an inhibitor in competitive inhibition
a
336
equation for compeitive inhibition
1/vo=(aKm/Vmax)1/[S]+1/Vmax
337
on the groah which line has no inhibitor
the lowest one
338
examples of competitive inhibitors
methanol poisoning, administer ethanol to allow time for the mathanol to be secreted by the kidneys so the alcohol dehydorgenase cannot act on it and turn it to formaldehyde
339
what changes with uncompetitive inhibition
both Vmax and Km
340
what happens during uncompetitive inhibition
inhibitor binds to enzyme substrate complex
341
what kind of graph do you get with uncompetitive inhibition
parallel slopes
342
what shows the influence of inhibitor in uncompetitive inhibition
a'
343
equation for uncompetitive inhibition
1/Vo=(Km/Vmax)1/[S] + a'/Vmax
344
what are the apparent values
what they appear to be when the inhibitor is present
345
what changes in mixed inhibition
both Km and Vmax
346
what happens in mixed inhibition
inhibitor can by to Enzyme or the Enzyme substrate complex
347
equation for mixed inhibition
1/Vo=(aKm/Vmax)1/[S] + a'/Vmax
348
are amino acid residues proton donors or acceptors
both
349
where do curly arrows start
at source of electrons making the new bond
350
enzyme classification 1.2.3.4
1 is the category
2 is what is does
3 is what it does it do
4 the number classified
351
what level of protein structure is HIV 1 protease
quaternary
352
is HIV 1 protease a hetero or homo dimer
homodimer
353
what are the substrates for HIV 1 protease
H2O and protein
354
what is the mechanism for HIV1 protease
general base catlaysis of water which attacks the carbonyl carbon and generates a tetrahedral intermediate that is stabilized by hydrogen bonding
the tetrahedral intermediate then collapses; the amino acid leaving group is protonated as it is expelled
355
what does the enzyme facilitae in HIV 1 protease
facilitate the direct attack of water on the peptide bond
356
what do the HIV 1 protease inhibitors do
inhibit the protease and then stops the virus
357
what is avoided when making drugs and why
chiral centers because it is too expensive
358
what does enolase do
general acid base catalysis and metal ion catalysis
359
mechanism for enolase
Lys345 abstracts a proton by general base catalysis,
2 of the Mg+ ions stabilize the resulting enolate intermediate
then glu211 faciliates elimination of the OH group by general acid catalysis
360
what does hexokinase do
induced fit, with the substrate present the enzyme will close up so no water can get out, but the enzyme will only close properly with correct substrate, glucose allows it to close but xylose wont
361
what is the first step in glycolysis
taking molecule of glucose and splitting it into 2 pyruvate
362
what happens with chymotripsin
4 amino acids are cut out, disulfide linkages hold the chains together, these are strong so they hold onto tertiary strucutre well, in primary strcuture 122 amino acids are apart but will fold
363
what do we need to do to study an enzyme
slow it down
364
what is the optimum pH of chymotrypsin
8
365
what are the speeds of the 2 steps of chymotripsin
first step is fast
second step is slow (this is where we have hydrolysis of acetic acid which was covalently linked)
366
first step of chymotripsin
enzyme releases paranitrophenol, but it gets stuck to the product
367
second step of chymotripsin
gets rid of the bound enzyme
368
what does kcat measure
speeds measured at turnovers ber second
369
how is chymotripsin activated
by proteolytic cleavage
370
what is proteolytic cleavage
must be cut to be activated
371
what does the biosynthesis of peptidoglycan require
enzyme transpeptidase
372
what is transpeptidase inhibited by
B-lactam antibiotics
373
what is b lactam
ring with 90 degree angles
374
what does transpeptidase usually do
usually attacks the carbonyl of a peptide bonds
375
what is peptidoglycan
mostly carbs held together by cross linking
376
gram positive vs gram neg bacteria
gram psoitive has thick cellular walls
377
how does peptioglycan contue to synthesize
by using trans peptidase for crosslinking
378
what does the Blactam do
it will stop the transpeptidase and gram positive bacteria
379
what has bacteria evolved to do that has caused problems
evolved to express B lactamases wjhoch are enzymes that can inactivate amoxilcillans and penicillans
380
what is a plasmid
order or 1000s base of DNA
381
what will the Blactamase do
attack B lactam
382
how can enzymes be regulated
allosteric enzymes
reversible covalent modifications
association with regulatory proteins
proteolytic cleavage
383
allosteric enzymes
additional binding sites when molecule binds it helps regulate
384
allosteric modulation
activity will diverge from michaleis menten behavior
385
less active enzyme
negative
386
more active enzyme
positive
387
what happens when something is bound to the allosteric site
can increase or decrease function
388
example of a covalent modification of an enzyme
phosphorylation
389
phosphoylation
regulation by presence based on Phosphate groups (can be truned on or off)
390
what enzyme sadd phosphates
kinases
391
what enzymes remove phosphates
phosphatases
392
what are the amino acid residues that can gain a phospahte
ones with OH groups
serine
threonine
tyrosine
histidine ** N can be phosphoylated
393
what is the coagulation cascade
blood clotting that includes several types of regulation to initiate and limit clotting
394
steps of the clotting process
1. activate platelets
2. acitivate fibrin monomer formation and polymerize
3. scab forms when polymerized fibrin cross links
395
what do activated platelets do
changes shape, they get more negatively charged phospholipids on surface and are triggered by an injury
396
what must fibrin undergo to work
proteolytic cleavage
397
injury
TF released by tissue to start the clotting process, activates several proteases, fibrin will catch platelets by crosslinking
398
why is Ca2+ used in the coagulation cascade
many steos used it, phospholipids are neagtive and are attracted to the calcium ions which helps them to interct with other proteins in the clotting process and will act as a bridge
399
what shuts down the coagulation pathway
prothrombin which is cleaved to thrombin, thrombin will activate C and S which stops the other activation factors
400
general formula for a carb
C(H2O)n
401
When is a carb in D form
furthest chiral carbon with hydroxy on the right
402
what is a carb
polyhydroxyl aldehyde or ketone
403
how to find the number of enantiomers of a carb
2^n
n=number of chiral centers
404
aldo sugar
carb with carbonyl on the end
405
keto sugar
carb with carbonyl on C2
406
what is more stable DNA or RNA and why
DNA is with one less O
407
what is the relationship between an aldohexose and a ketohexose
isomers
408
what does chirality look like in monosaccarhides
all monosaccharides except for dihydroxyacetone contain 1 or more chiral carbon atoms
409
what is the difference in naming for pentoses
Ribose refers to aldo sugars and ribulose refers to keto sugars
410
order of hydroxyl groups in glucose
RLRR
411
what is an epimer
structure differs in the configuration at one chiral center
412
beta vs alpha on a cyclic monosaccharide
beta is OH up
alpha is OH down
413
anomeric carbon
carbon attached to 2 oxygens in the ring, used to be the carbonyl carbon
414
a way that hemoglobin can be separated from glycated hemoglobin
electrophoresis
415
normal glucose in blood in mM
5mM
416
normal glucose in blood based on hospital units
90 mg/dL
417
how do you get glycated hemoglibin
when hemo reacts with glucose
418
what does it mean if there i 5mM of glycated hemoglobin
5% of the hemoglobin is gycated
419
how much glcated hemoglobin is there in uncontrolled diabetes
7-10%
420
pre diabetic range
100-120
421
diabetic range
<120
422
what happens with more oxidized glucose in the blood
the O2 must be reduced to hydrogen peroxide so enzyme test strips take the hydirgen peroxide and interact with some colorless compoind will interacts with peroxidase, the colorless compound will turn a colored product
423
disaccharide
2 monosaccharides joined by an O glycosidic bonds (elimination of H2O)
424
for dissacahrides what do you loose when you connect them
loose an Oxygen from anomeric C
425
where is lactose found
in milk
426
what makes up lactose
glucose and galactose
427
is lactose a reducing sugar
yes bc it has a free anomeric Carbon
428
where is sucrose found
in table sugar
429
what is sucorse formed by
plants
430
what makes up sucrose
glucose and fructose
431
is sucrose a reducing sugar
no bc anomeric carbon is locked in the glycosidic linkagw
432
where is trehalose found
in the hemolymph of insects
433
what makes up trehalose
2 molecules of glucose
434
is trehalose a reducing sugar
no the 2 moelcuels of glucose link the C1 together
435
what makes something a reducing sugar
is the anomeric carbon is all tied up then it cannot be a reducing sugar
436
what can a happen t reducing sugars
can be oxidized and then can act as a reducing agent to something else
must be able to be oxidized with a free anomeric C
437
why does the reducing sugar need a free anomeric carbon
so that the carbon can go from aldehyde to carboxyilic acid
438
why does sweetness occur
sweet taste is detected by receptors in the T1R2 and T1R3 in the plamsa membrane of gustatory cells in the taste buds on the tongue, bind to proteins receptor in tase bud on tongue and excite the protein coupled receptor
439
what is special about aspartame as a artificial sweetner
looks like a protein, is a dipeptide, no c terminus but has a methyl group to make a methyl ester
440
what artificial sweetner has the same chemcial formula as glucose
sorbital
441
what is different about sorbital
no aldehyde or ketone so it cant become a ring, it stays linear so our body can't break down the whole thing, can lead to diahrrea, cant be absorbed too many solutes present so water stays in the intestine
442
what do the proteins and lipids on the surface of red blood cells do
present for a specific groupn
443
what is the universal recipient
AB, can recieve any blood
444
what can type B receive
B or O
445
what can type A receive
A or O
446
universal donor
O
447
whawhat is the possibility for making more type O blood from other types
removing the final monosaccahride unit, tru and find enzyme that break the glycosidic linkage to turn type A into type O
448
what are most carbs in nature
polysaccharides
449
what must you identify in a polysaccahride
if the monosaccahirdes are homo or hetero polysaccahrises
the length of chain
bonds linking the units
degree of branching
450
what are polysacchairdes used for
storage for fuel and structural elements
451
what linkages are locked in starch
alpha
452
what is starch a polysaccarhide of
glucose
453
what is starch made up of
amylose and amylopectin
454
branching of amylise
unbranches a1-4 linkages
455
branching of amylopectin
branched a1-6 every 24-30 residues
456
branching in glycogen
8-12 residues
457
what are dextrans made in
bacteria and yeast
458
what is the branching is dextrans
branched homo polysaccahride of glucose
a1-6 linkages, also a1-2 and a1-4
459
what is peptidoglycan made from
repeating polysaccahirde of N acetyl glucosamine and n acetyl muramic acid, hetopolysaccahirde
460
what does the peptido mean is peptidolgycan
cross linked by D amino acids
461
what does a lysosyme do
breaks glycosidic bonds by hydrolysis
462
where is starch made
in plants
463
where is glycogen made
in animals
464
what is starch and glycogen
storage polysaccahride in either plants or animals
465
bonding in starch
does not hydrogen bond well, it would form a helix if it did this
466
what makes up glycogen
all glucose
467
branching in glycogen
a 1-4 linkages
a1-6 branches, branches every 8-12 residues
468
does glycogen or strach attract water
glycogen
469
what is the plant structural polysaccharide
cellulose
470
where is cellulose found
cell walls of plants, woods, cooton
471
what kind of strucutre does cellulose form
linear
472
what will break B1-4 glycosidic linkages in cellulose
wood fungi
473
bonding in cellulose
forms hydrogen bonds on itself
474
what makes up cellulose
glucose
475
where is chitin found
exoskeleton of insects
476
what makes up chitin
linear N-acetylglucosamine
477
linkages in chitin
all B becuase the molecule sometimes flips so lots of B linkages will from a linear strong dry strucutre
478
does a or B hold on to water and why
alpha bc it is looser
479
what is agar
mixture of sulfated heteropolysaccahrides, extracted from marine algea and seaweed
480
what is agarose
the component of agar with the fewest charged groups (sulfates and pyruvates)
481
what is the repeating unit in agar
galactose and a fused 6 member to 5 member ring, heteroolysaccahride
482
what are glycosaminoglycans
carbs with amino groups
483
are glysoaminoglycans intracellular or extracellular
extracellular
484
are glycosaminoglycans hetero or homopolysaccahirdes
hetero
485
are glycosaminoglycans positive or negative
negative forces extedned conformations
486
what do glycosaminoglycans provide
viscosity, adhesiveness, and tensile strength to extracellular matrix
487
examples of glycosaminoglycans
hyaluron, chondroiton sulfate, keratan sulfate, purified heparin
488
hylauron
vitreous humor of the eye
489
chondroiton sulfate
catilage, tendons and ligaments
490
keratan sulfates
cornea, cartilage, bone and horny structures
491
purified heparin
prevents blood clotting
492
defects of glycosaminoglycans
synthesis or degradation
493
example of a synthesis defect of glycsoaminoglycans
bone spur growth caused by the inability to add GlcNAc-GlcA to heparin sulfate chain
the cabs arent added correctly then bone develops extra bone growth
494
what are role dextrans
strucutral in bacteria and extracellualr adhesive
495
role of agarose
structural in algea
496
role of hylauron
structural
497
what are glycoconjugates
carbohydrates as information carriers including cell-cel communication and transportation
498
what makes up a glycoprotein
little bit of carb lots of protein
499
what does it mean to be o linked
attach to oxyegn on serine or threonine
500
what does it mean to be N linked
only to N in an Asn residue must happe where N{P}-[S/T]
501
what is a lipopolysaccahirde
Lipid A is found in the outer membrane of gram negative bacteria
502
what do influenza treatments binds to
sialic acid binding site o neuraminidase (NA)
503
how to analyze carbs
must first detatch the carb from the protein an enzyme will help to break that linkage, once separaed the info has to be pieced back together
504
mass spec analysis of complex carbs
get fractionation and piece the monosaccharide together
505
gene
segment of a DNA molecule that contains information required for the synthesis of a functional biological product i.e. protein or RNA
all the DNA that codes for a single functional polypeptide chain
506
chromosome
single large DNA moelcule and its associated proteins (and often regulatory and structural RNA) containing many genes
507
normal number of chromosomes in humans
46
508
nucleotide
all 3 parts: base, ribose and phosphate
509
nucleoside
base and ribose
510
where is the base attached to in a nucleotide
c1
511
where is the phosphate attached to in a nucleotide
c5
512
purine shape
2 rings
513
pyrimidine shape
1 ring
514
what are the purines
adenine guanine
515
what are the pyrimidines
cytosine
uracil
thymine
516
what is the least polar part of the nucleotide
base
517
characteristics of all bases
aromatic
planar
neutral (no charge)
518
sp2 geometry
tirgonal planar
519
sp3 geometry
tetrahedral
520
what conditions is RNA hydrolyzed in
alkaline
521
what is alkaline conditons
basic
522
UV absorbance of DNA
260 nm
523
base composition between species
varies
524
compoisiton between different tissues of same species
same composition
525
base composition does not change with
age, nutrition, or changing environment
526
what does DNA form
stable double helix
527
what is the largest width of DNA
20A
528
how long is a complete turn of DNA
36 A
529
what cnonects the bases in DNA
phosphodiester bonds link C3 to C5 of the ribose ring
530
which bases pair together and how many bonds
A-T/U (2)
G-C (3)
531
replication of DNA
each parents strand acts as a template for the biosynthesis for complementary daughter strands
532
endo
means C2 or C3 on the ribose is up
533
exo
means C2 or C3 on ribose is down
534
the DNA backbone is stiff or flexible
flexible
535
common forms of DNA
A
B
Z
536
A form of DNA
dehydrated DNA (often in crystal structures)
537
B form of DNA
most common/stable for random sequence
538
Z form of DNA
occurs with alternating pyrimidines and purines ie (CG)n sequnece
539
weight difference between A, B, Z form
all weigh the same
540
what hand is the B form
right handed
541
diameter of the B form
20A
542
base pairs per helical turn of the B form
10
543
helix rise per base pairs in B form
3.4A
544
base tilt normal to the helix axis
6 degrees
545
sugar pucker conformation of the B form
C-2 endo
546
glycosyl bond conformation of the B form
anti
547
what does palindrome mean
DNA sequence is complementary to itself
548
what is a way that DNA denatures
heated beyond melting temp
549
term for DNA strands separating
denaturing
550
term for DNA strands going back together
annealing
551
when DNA denatures is there an increase or decrease in viscosity
decrease
552
ways to disrupt hydrogen bonds
heat
pH extremes
553
what does metling temp of DNA depend on
pH and ionic strength of the solution in addition to GC content
554
how can DNA denaturation be monitored
viscosity measurements or UV measurements
555
hyperchrombic effect
increase in UV absorbption
556
deamination
NH2 to a =O
557
depurination
lose a base
558
what is more common deamination or depurination
deamination
559
what are ways that DNA can be damaged
Deaminating agents
alkylating agents
oxidative damage
560
deaminating agents
nitrates and nititres are often used as perservatives and can result in nitrous acid which accelerates deamination reactions
561
alkylating agents
add carbon containing group to be added to bases preventing base pairing
562
oxidative damage
H2O2, OH radicals, O2- cause oxidation of deoxyribose strand breaks and oxidation of bases
563
what can form prymidine dimers
UV damage
564
what is more stable ds DNA or dsRNA
dsRNA
565
mRNA
transfers genetic info from DNA to ribosome, forms a single stranded helix with base stacking
566
tRNA
single stranded with significant hyodgren bonds, some regions with helix, ltos of non standard hydorgen bonds
567
rRNA
in ribisomes, site of protein synthesis
568
enzyme cofactors in nuceltides
helps enzyme function
569
what does adenosine do in the nuecleotide
does not participate directly in the primaru function but is required for the cofactor or substrate to bind to the enzyme
570
what else can enzyme co factors be
energy cofactors:ATP
571
why are the nucleitide co factos so large
only involve the one potion, but the large cofactor allows for more affintity it can have for the enzyme,
572
why do the products in ATP breakdown have lower energy then the substrates
more products then substrates entropy goes from 2-->3 so more disorder (lower entrioy = more disorder)
substrates are highly strained -4 on ATP and is releiced on the ADP
more resonance structures on HPO42- (more stable)
573
special about DNA synthesis
chemical synthesis
574
is DNA synthesis automated or manual
automated
575
what end of the strand is DNA syntheized from
3'
576
primer
short sequence of DNA, chemcially syntheiszed, happens very quick and cheap with increased accuracy
577
what is needed for DNA syntheiss
protecting groups
578
what is PCR
polymerase chain reaction
579
what is needed for PCR
template DNA
primers (forward and reverse)
dNTPs (building bocks)
Thermostable DNA polymerase
thermocycler
580
polymerase
enzyme that reads template and makes copies
581
what does the thermostable DNA polymrase do
synthesizes the 2 new strands, work at 72 degrees C
582
why is it important for the polymerase to work at high temps
it wont unfold at high temps
583
what does the thermocyler do
instrument that carefully controls temp
584
how does DNA polyemrase know when to stop
it doesnt, 1st, 2nd, 3rd long peices but later rounds will be correct size bc it cant go any furhtr
585
what is needed for DNA sequencing by the sanger methods
template DNA to be sequenced
primer DNA sequence
dNTPs
ddNTPs
DNA polymerase
586
why is ddNTP needed for sanger DNA sequencing
cayses DNA syntheis to stop bc there is no O to continue
587
limitations to sanger sequencing
too slow and requires primers
588
imporvements of 1st gen sanger sequencing
can be done in 1 tube, separate sizes with specific analysis. each base has a different lable
589
what can the new novaseq do
seqience 45 whole genomes at once
average a human gemome per hour
current cost is 1000$ oer genome
590
what does illumina sewuencing make use of
flurescent lables, much more sensitive than absorbance measures
591
what is not needed in illumina sequencing
primers
592
limitations of SMRT sequencing
polymerase gets electrocuted or falls off
loading long pieces of DNA
593
SMRT sequencing steps
long sewuence of DNA flow cell--> immobilize DNA pol in the flow site --> in a circle so it can be read multiple times --. flourescent lable on the phopshate
594
what is the central dogma
DNA is transcribed into RNA which is translated to a protein
595
what must happen for DNA cloning
separating a specific gene or DNA segment from a larger chromosome
596
what do we do with the separated gene in DNA cloning
attach it to a smaller molecule of DNA like a plasmid or vector
597
what do we do to get the DNA to replicate
replicate it millons of times by introducing it into a fast multiplying host
598
what must happen for the DNA to be taken up by the plasmid
weaken the hydrophobic effect with heat
599
what is the first step of cloning
use restriction enzymes to cleave cloning vector (plasmid)
600
what is the second step of cloning
obtain specific gene to interest "insert" from chromosome of organism of interest via PCR and cleave with same restriction enzyme
601
what is the third step of cloning
ligate the DNA fragments
602
what is the 4th step of cloning
transform bacterial host cell
603
what is the 5th step of cloning
selectively multipy host cell in antibiotic containing media
604
what do plasmids contain
multiple cloning sites
605
why is it good that plasmids have lots of cloning sites
allows you to use different enzymes (enzymes used with buffers that work with both in optimal conditions)
put sticky ends on genes of interest (cut ends wihtou cutting out gene of interest (need options for where to cut)
606
what types genes do some plasmids contain
antibiotic resistent genes
607
genome
all the genetic information contained by an organism: genes + regulatory sequneces + non coding DNA
608
how much of the human genome is composed of exons
1.5%
609
exons
coding DNA
610
how much of the human genome is introns
28.5%
611
what percent of our human genome is not genes
70%
612
what becomes part of the final mRNA
exons
613
how many base pairs make up a nucleosome
146
614
how many proteins make up the nucleosome
8
615
how many proteins make up the nucleosome
8
616
what are histone proteins modified by
methylation, acetylation/deactylation, and phosphorylation
617
what part of the histone does the DNA actualy wrap around
H1
618
other parts of the HIstone
2 of H2A, H2B, H3, H4
619
dsDNA--> RNA
transciption
620
what type of RNA is transcribed
messenger RNA
621
what is used to synthesize the RNA comp strand to template strand of duplex DNA
DNA dependent RNA polymerase uses ribonuceoside 5' triphosphate
622
where does the RNA polymerase bind
to the promoter sequence at the 5' end of the gene to be transcribed
623
where does transcription end
termination sequence
624
orientation of the template strand
3'-5'
625
mRNA synthesized in what orientation
5'-3'
626
what do the Mg ions do in transcirption
co factors, DNA is neg so Mg will gelp hold it in the active site
627
mRNA --> protein
translation
628
what direction is mRNA read
5' to 3', one codon at a time protein syntheiszed N to C term
629
is tranaltion fast or slow
fast and accurate
630
what is mRNA read by
adapter tRNA molecules
631
where does translation occur
ribosome
632
what percent of the ribosome is rRNA
65%
633
what percent of the ribosome is protein
35%
634
what is challenge for getting the crytal structure of rRNA
need crystal strucutre of all the prtoeins involed , must separate and collect fragments by centrifugation
635
the genetic code is
nearly universal
636
how many different tRNAs are there
32
637
what is the sequence of bases on the end of a tRNA adapter molecule
anticodon
638
what direction is the anticodon read
3'-5'
639
at what end of the trNA is the amino acid
3'
640
why is it good that we only have 32 tRNAs
speed (dont need to test as many tRNAs)
weaker bonds allow for quicker dissociation
641
how are amino acids activated
the tRNA is aminoacylated
642
initiation for tranlation
the mRNA and aminoacylated tRNA bind to the small ribosomal subunit, the large subunit then binds
643
elongation for translation
succesive cycles of aminoacylated tRNA binding and peptide bond formation occur until the ribosome reaches a stop codon
644
termination in translation
translation stops when a stop codon is encountered. the mrna and protein dissociate and the ribosomal subunits are recycled
645
last part of tranlation
protein folding and postranslation processcing
646
what happens in post translational processing
sugars added, 1st tRNA amino acid is cut
647
start codon
AUG
648
what is a polysome
multiple ribosomes can be attached to the RNA
649
what do most lipids contain
faty acids
650
whatt is a fatty acid
carboxylic acid, long hydrocarbon chain (nonpolar), even number of carbons (usually), somes unsaturated (non conjugated, cis double bonds)
651
what is an explicit double bond
Sp3 carbon inbetween Sp2 C , not conjugated
652
what does melting point and solubility of fatty acids depend on
depends on chain length and degree of saturation
653
what type of interactions cause fatty acids to associate
weak
non covalent
654
saturated fatty acid
very solid, no double bonds, well packed
655
unsaturated fatty acid
has double bonds, more liquid bc of the kink formed by the double bond
656
what is the melting point of a fatty acid with more double bonds
higher melting point
657
what is the melting point of a longer fatty acid
longer they are the higher the melting point
658
triacylglycerol or triglyceride
glycerol and 3 fatty acids linked by ester bonds
659
where are triglycerides stored
in fat cells called adipocytes
660
how much energy can be stored in lipids
weeks to months of energy sotred
661
what do biological membranes consist of
lipid bilayer
662
characterisic of membrane lipids
amphipathic (polar and non polar ends)
663
what are the. 5types of membrane lipids
glycerophospholipids
galactolipids and sulfolipids
archeal tetraether lipids
sphingolipids
sterols
664
what holds lipids together in the bilayer
hydrophobic effect (non polar tails away from water)
665
what keeps a singular lipid together
covalent bonds
666
lot or little entropy in the lipid bilayer
lots (all are constantly moving around, have lots of freedom)
667
what is a phospholipid composed of
phosphate
glycerol
fatty acid tail
668
glycerophospholipid or phosphoglycerides
2 fatty acids + glycerol + phosphate + head group
669
what part of the lipid determines the net charge on moelcuels
head group
670
galactoplipids and sulfolipids
polar head group is galactose or glucose with or without a sulfate group. common in plants where soil phosphate supply may be limited
671
archeal lipids
8 isoprene units per chain
ether linkage is very stable
thirve in extreme conditions
672
what is special about archeal lipids
monolayer all nonpolar parts in middle, both ends are polar
673
why wont archeal lipids melt apart
lots of branch points built fro 5C isoprene unit
