Class One Flashcards
1
Q
forms of energy in chemistry (x2)
A
kinetic and potential
2
Q
kinetic energy
A
movement of molecules
3
Q
potential energy
A
energy stored in chemical bonds
4
Q
first law of thermodynamics
A
energy of the universe is constant
e.g. when energy of a system decreases, energy of surroundings has to increase
5
Q
second law of thermodynamics
A
entropy of the universe tends to increase (spon. reactions increase disorder)
6
Q
what does a negative change in entropy mean
A
lost entropy = disorder has decreased
7
Q
Gibbs free energy equation
A
8
Q
enthalpy equation
A
delta H = delta E + (P x delta V)
9
Q
free energy relationship with enthalpy and entropy
A
free energy increases with increased enthalpy + decreases with increased entropy
10
Q
which reaction is more favourable: decreased or increased delta G
A
decreased (means that there is high entropy)
11
Q
spon. reactions: neg or pos delta G
A
negative
12
Q
exergonic reactions
A
reactions with neg delta G: energy exits the system
13
Q
endergonic reactions
A
reactions with pos delta G: only occur if energy is added
14
Q
exothermic reactions
A
reactions with neg delta H (enthalpy) → release heart
15
Q
endothermic reactions
A
reactions with pos delta H → require an input of heat
16
Q
Gibbs free energy and equilibrium equation
A
17
Q
what is K
A
ratio of products to reactants during equilibrium
18
Q
difference between lnK and lnQ in Gibbs free energy equation
A
lnK is used when equilibrium has been reached
lnQ is used at any point of time
19
Q
removal of reactant/product & its effect on Q and Keq
A
causes a change in Q but not Keq
20
Q
delta G = 0
A
reaction is at equilibrium
21
Q
spontaneous reaction & delta G
A
spon. reactions have a neg delta G
22
Q
spontaneity and reaction rates
A
a spon reaction means it is energetically favourable but says nothing about the rate of reaction
23
Q
what is activation energy
A
the energy required to produce the transition state (very unstable)
24
Q
what is a catalyst
A
something that lowers the Ea without changing the delta G
25
how does a catalyst work
lowers Ea by stabilizing the transition state → makes it less thermodynamically unfavourable
\*never consumed in a reaction
26
photosynthesis definition
process in which plants store energy from the sun in the bond energy of carbohydrates
27
photoautotrophs
something that uses energy from light to make their own food
28
chemoheterotrophs
something that uses the energy if chemicals produced by other living things (e.g. plants & animals)
29
oxidation reactions
gain of oxygens atoms
loss of hydrogen atoms
loss of electrons
30
reduction reactions
loss of oxygen atoms
gain of hydrogen atoms
gain of electrons
31
redox pair
when one atom gets reduced, another must be oxidized
32
catabolism
process of breaking down molecules
33
anabolism
building up metabolism
34
are anabolic reactions usually reductive or oxidative
reductive
e.g. fatty acid are generated by the successive reductions of a carbon chain
35
Bronsted-Lowry acids and bases
acids are proton donors (H+)
bases are proton acceptors
36
Lewis acids and bases
acids are electron pair acceptors
bases are electron pair donors
37
Lewis acid/base reactions usually occur due to the formation of…
coordinate covalent bonds
38
biological example of a coordinate covalent bond
oxygen binding to the iron atom in a heme group
39
conjugate base
remaining structure after a B-L acid donates an H+
40
conjugate acid
reminding structure after a B-L base bonds with H+
41
difference between a B-L acid & its conjugate base
base is missing an H+
42
difference between a B-L base and its conjugate acid
acid has an extra H+
43
strength of an acid formula
conc. of products over reactants
44
what is Ka
the acid-ionization constant of an acid
aka the equilibrium expression for an acid-dissociation reaction
45
strength of a base formula
conc. of products over reactions
46
polyprotic
a substance that has more than one proton to donate
47
amphoteric substance
something that can act as an acid or base
48
what is always amphoteric
conjugate use of a weak polyprotic acid
(can either donate or accept another proton)
49
why is HCO3- a weaker acid than H2CO3
every time a polyprotic acid donates a proton, the resulting compound will be a weaker acid than the one before
50
pH of an acid formula
pH = -log[H+]
51
pOH of a base fomula
pOH = -log[OH-]
52
pH and pOH relationship
pH + pOH = 14
53
pKa and pKb
pKa = -logKa
pKb = -logKb
54
pKa/pKb and strength
the lower the pKx, the stronger the acid/base
55
what is a buffer
a solution that resists changing pH when a small amount of acid/base is added
56
most important buffer system in blood plasma
bicarbonate buffer system
57
bicarbonate buffer system
H2CO3 → H+ + HCO3-
58
how is carbonic acid formed
byproduct of cellular respiration (CO2) combines with water
59
what is Gibbs free energy
amount of energy in a reaction available to do chemical work
60
protein composition
20 different amino acids linked together in polymers
61
generic formula for amino acids
variable R group
x-amino group
tetrahedral x-carbon
x-carboxyl group
62
unique feature of each amino acid
it's side chain! gives it it's physical/chemical properties that distinguish it from the other 19 AAs
63
acidic amino acids (x2)
aspartic acid: asp (D)
glutamic acid: glu (E)
64
why are some amino acids classified as acidic?
they have carboxylic acid functional groups in their side chains → acidic
65
in acidic amino acids, how many functional groups can act as acids
three!
the 2 backbone grows and the R group
66
what are asparate and glutamate
anionic (deprotonated) forms of the acidic AAs
this is how they are observed at physiological pH
67
basic amino acids (x3)
lysine: lys (K)
arginine: arg (R)
histidine: his (K)
68
pKa values of the side chains in basic AAs
lys (K): 10
arg (R): 12
his (H): 6.5
69
why is histidine unique
has a side chain with a pKa close to physiological pH
classified as a base but can act as both
70
hydrophobic (non polar amino acids) (x7)
glycine: gly (G)
alanine: ala (A)
valine: val (V)
leucine: leu (L)
isoleucine: ile (I)
phenylalanine: phe (F)
trypyophan: trp (W)
71
AAs with aliphatic (alkyl) side chains
non polar AAs
gly, ala, val, leu and ile
72
AAs with aromatic side chains
phe, trp (non polar)
and try (polar)
73
hydrophobic group & force
the larger the hydrophobic group, the greater the hydrophobic force repelling it from water
74
polar amino acids (x5)
serine: ser (S)
threonine: thr (T)
tyrosine: tyr (Y)
asparagine: asn (N)
glutamine: gln (Q)
75
what makes an AA polar
has an R group that is polar enough to from hydrogen ions with water but does not act as an acid or base
76
which AAs are modified by the attachment of a phosphate group by a kinase
serine, threonine + tyrosine (polar)
this modification is important → regulates protein activity
77
sulfur-containing amino acids (x2)
cysteine: cys (C)
methionine: met (M)
78
properties of cysteine
contions a thiol (alcohol with a S atom instead of O)
polar
79
properties of methionine
contains a thioether (ether with a S instead of O)
non polar
80
proline
has an amino group that is covalently bound to its non polar side chain → creates a secondary alpha amino group
important in protein folding
81
what are essential AAs
AAs that cannot be synthesized by humans → must be obtained by diet
82
nine essential amino acids
lysine
histidine
threonine
valine
leucine
isoleucine
phenylalanine
tryptophan
methionine
83
what 2 groups do AAs contain
acidic carboxylic group
basic amino group
84
zwitterion
a molecule with positive and negative charges that balance → no overall net charge
85
the pH of which a molecule is uncharged is..
the isoelectric point (pI)
86
how to calculate the pI of a molecule with 2 functional groups
average the pKas of the 2 functional groups
87
what is a peptide bond
links amino acids together
formed between the carboxyl group of one AA and the alpha-amino group of another AA (loss of water)
88
backbone of a polypeptide
N-C-C-N-C-C pattern formed from the AAs
89
when is an individual AA termed a residue
when it is part of a polypeptide chain
90
N-terminus
amino end of a polypeptide
91
C-terminus
carboxylic acid end
92
proteolysis/proteolytic cleavage
hydrolysis of a protein by another protein
93
what is a proteolytic enzyme/protease
the protein that does the cutting in proteolysis
94
which peptide bond is usually cleaved by enzymes
the peptide bond adjacent to a specific AA
95
which amino acid can form disulphide bonds
cysteine
96
how is a disulphide bond formed
thiol of one cysteine reacts with the thiol of another cysteine to make a covalent sulfur-sulfur bond
97
purpose of a disulphide bond
stabilizes tertiary protein structure
98
cystine vs cysteine
once a cysteine residue becomes disulfide-bonded to another cysteine residue, it becomes cystine
99
what is denaturation
the disruption of a protein's shape without breaking peptide bonds
100
conditions in which proteins are denatured (x4)
urea (disrupts hydrogen bonding interactions)
extremes of pH
extremes of temperature
changes in salt conc.
101
primary protein structure
AAs bonded to each other in the polypeptide chain aka sequence
102
secondary protein structure
folding of polypeptide chain into shapes stabilized by hydrogen bonds between backbone NH and CO groups
103
2 types of secondary protein structures
alpha helix
beta pleated sheet
104
why do proline residues never appear within the alpha helix
the formation of a peptide bond with proline eliminates the only H on the N (disrupts the backbone H-bonding in the polypeptide chain)
kinks the polypeptide chain
105
why is an alpha helix a favourable structure for a hydrophobic transmembrane region
all the polar NH and CO groups in the backbone are H-bonded to each other in the inside of the helix and so don't interact with the hydrophobic membrane interior
106
hydrogen bonding in beta pleated sheets
H-bonding occurs between residues distant from each other or on separate polypeptide chains
107
types of beta sheets
parallel pleated sheet: adjacent polypeptide strands running in the same direction
antiparallel pleated sheet: polypeptide strands running in opposite directions
108
tertiary protein folding
3D shape of a protein
109
what drives the folding into tertiary structures
interactions of R groups with each other and with the solvent (water)
110
hydrophobic R groups (tertiary)
tend to fold into the interior of the protein (away from the solvent)
111
hydrophilic R groups (tertiary)
tend to be exposed to water on the surface of the protein
112
hydrophobic effect
how hydrophobic/philic R groups tend to fold
113
quaternary protein structure
interactions between polypeptide subunits
the arrangements of subunits in a multisubunit complex is quaternary structure
114
forces that stabilize tertiary and quaternary structures
van der Waals
hydrogen bonds
disulfide bonds
electrostatic interactions
115
what does a hydrolase do
hydrolyzes chemical bonds
116
what does an isomerase do
rearranges bonds within a molecule to form an isomer
117
what does a ligase do
forms a chemical bond
118
what does a lyase do
breaks chemical bonds by means other than oxidation or hydrolysis
119
what does a kinase do
transfers a phosphate group to a molecule from a high energy carrier, such as ATP
120
what does an oxidoreductase do
runs redox reactions
121
what does a polymerase do
polymerization
122
what does a phosphatase do
transfers a phosphate group to a molecule from inorganic phosphate
123
what does a protease do
hydrolyzes peptide bonds
124
what is reaction coupling
a favourable reaction is used to drive an unfavourable one
125
why is reaction coupling possible
free energy changes are additive
126
how does ATP hydrolysis drive unfavourable reactions (x2)
causes a conformational change in a protein
transfer of a phosphate group from ATP to a substrate
127
how are carbohydrates broken down to CO2
oxidation (aka combustion or burning)
128
why are carbohydrates the principle energy source for cellular metabolism
the oxidation of carbohydrates to CO2 releases large amounts of energy
129
what is a monosaccharide
a single carbohydrate molecule → aka simple sugar
130
monosaccharide formula
CnH2nOn
131
examples of monosaccharides
fructose, glucose, ribose
132
monosaccharides to polysaccharide
monosaccharide → disaccharide → oligosaccharide → polysaccharide
133
what is a glycosidic linkage
bond between 2 sugar molecules
covalent bond formed in a dehydration reaction (requires enzymatic catalysis)
134
glycogen and starch
glycogen → energy storage in animals
starch → energy sto=rage in plants
135
cellulose
polymer of cellobiose
cellobiose does not exist freely in nature (only as cellulose)
wood + cotton are made of this
136
roles of lipids
in adipose cells, triglycerides store energy
in cellular membranes, phospholipids constitute a barrier between intracellular and extracellular environments
cholesterol serves as the building block for hydrophobic steriod hormones
137
fatty acid structure
composed of long unsubstituted alkanes that end in a carboxylic acid
138
why are only even numbered fatty acids made in human cells
they are synthesized 2 carbons at a time from acetate
139
saturated vs unsaturated fatty acids
saturated: no C=C bonds, bound to maximum Hs
unsaturated: one or more double bonds (almost always Z aka cis)
140
what drives hydrophobic tails into the center of a micelle
hydrophobic interaction
141
composition of a triglyceride
3 fatty acids esterified to a glycerol molecule
142
why is it important to store fatty acids as triglycerides
free fatty acids are reactive chemicals
143
what enzyme hydrolyzes fats
lipases
144
why are fats more efficient energy storage molecules than carbohydrates
packing and energy content W
145
packing - fats
the hydrophobicity of fats allows them to pack together closer than carbohydrates
146
energy content - fats
fat molecules can store more energy than carbohydrates (more energy carbon-for-carbon than a carbohydrate)
147
what are membrane lipids
phospholipids derived from diacylglycerol phosphate
148
how is a lipid bilayer formed
hydrophobic interactions drive the formation of the bilayer and stabilized by van der Waals forces between the long tails
149
why do unsaturated fatty acids prevent a solid membrane
unsaturation in phospholipid fatty acids increases membrane fluidity → disrupts orderly packing of hydrophobic lipid tails
150
what increases membrane fluidity
decreasing the length of fatty acid tails
double bonds in phospholipid fatty acids
cholesterol
151
how does cholesterol affect membrane fluidity
at low temps → increases fluidity (membrane antifreeze)
at high temps → reduces membrane fluidity
152
terpenes
compounds built from isoprene units
formula: (C5H8)n
153
how are terpenes classified
they can be linear or cyclic and are classified by the number of isoprene units they contain
mono = 2
sesqui = 3
di = 4
154
squalene
a triterpene (6 isoprene units) and it is used in the manufacture of steroids
155
what is a terpenoid + example
species built from an isoprene skeleton & functionalized with other elements (O, N, S)
vit A
156
what are steroid hormones made of + examples
cholesterol
testosterone and estradiol
157
structure of steroids
tetracyclic ring system
158
where does cholesterol come from
diet + synthesis in liver
159
how is cholesterol carried in the blood
packaged with fats and proteins into lipoproteins
160
characteristics of phosphoric acid
inorganic (doesn't contain carbons)
can donate 3 protons
161
orthophosphate
aka just phosphate
162
pyrophosphate
2 orthophosphates bound together via an anhydride linkage
163
why do the phosphate anhydride bonds store so much energy
when phosphates are linked together, their negative charges repel each other
orthophosphate has more resonance dorms (lower free energy than linked phosphates)
orthophosphate has a more favourable interaction with water than linked phosphates
164
composition of nucleotides
ribose sugar group
purine/pyrimidine base joined to carbon 1
1 or 2 or 3 phosphate units joined to carbon 5
165
ATP phosphoanhydride bonds
energy extracted from the oxidation of food is immediately stored here → later used to power cellular processes
166
maltose
glucose + glucose
167
sucrose
glucose + fructose
168
lactose
glucose + galactose
169
4 lipids in the body
triglycerides
phospholipids
terpene
cholesterol
170
importance of folding in enzyme function
for the proper formation of the active site → directly involved in catalysis
171
active site model
states that the substrate and active site are perfectly complementary
172
induced fit model
states that the substrate and active site differ and that the binding of the substate induces a conformational change in the enzyme
173
stereospecificity
the ability to distinguish between stereoisomers
174
aspartic acid
asp (D)
acidic AA
175
glutamic acid
glu (E)
acidic AA
176
lysine
lys (K)
basic AA
177
arginine
arg (R)
basic AA
178
histidine
his (H)
basic AA
179
glycine
gly (G)
hydrophobic + non polar
180
alanine
ala (A)
hydrophobic + non polar
181
valine
val (V)
hydrophobic + non polar
182
leucine
leu (L)
hydrophobic + non polar
183
isoleucine
ile (I)
hydrophobic + non polar
184
phenylalanine
phe (F)
hydrophobic + non polar
aromatic
185
tryptophan
trp (W)
hydrophobic + non polar
aromatic
186
serine
ser (S)
polar
187
threonine
thr (T)
polar
188
tyrosine (Y)
tyr (Y)
aromatic
189
asparagine
asn (N)
polar
190
glutamine
gln (Q)
polar
191
cysteine
cys (C)
sulfur containing
192
methionine
met (M)
sulfur containing
193
proline
pro (P)
has a ring structure
194
characteristics of proteases
have an active site with a serine residue whose OH group can act as a nucleophile (attack the carbonyl carbon of an AA residue in a polypeptide chain)
195
what is a recognition pocket
pocket in an enzyme's structure that attracts certain residues on substrate polypeptides
196
cofactors - enzymes
metal ions/small molecules that are required for activity in many enzymes
197
an organic cofactor is a…
coenzyme
198
4 ways to regulate enzyme activity
covalent modification
proteolytic cleavage
association with other polypeptides
allosteric regulation
199
covalent modification
different groups attached to proteins that regulate their activity
e.g. phosphoryl group (added by a protein kinase) can activate/inactivate an enzyme
200
action of protein phosphatase
reversal of protein phosphorylation
201
proteolytic cleavage
inactive forms (zymogens) are activated by cleavage by a protease
202
association with other polypeptides
some enzymes have catalytic and regulatory subunits
some proteins require association with another peptide to function
203
allosteric regulation
modification of active-site activity through molecules with other specific sites on the enzyme (allosteric sites)
alters the enzyme to increase/decrease catalysis
204
negative feedback/feedback inhibition
end product will shut off an enzyme early in the pathway
205
feedforward stimulation
stimulation of an enzyme by its substrate or a molecule used in the synthesis of the substrate
206
enzyme kinetics
study of the rate of formation of products from substrates in the presence of an enzyme
207
reaction rate
amount of product formed per unit time
208
Vmax
the reaction rate at which the enzyme is saturated
adding substrates doesn't increase the reaction rate
209
Michaelis constant
the substrate conc. where the reaction velocity is half its maximum g
gives info about the affinity of an enzyme for its substrate
210
what does a low Km mean
not much substrate is needed to get the reaction rate to half the maximum rate
enzyme has a high affinity for the substrate
211
cooperativity
binding of substrate to one subunit modulates the affinity of other subunits for substrate
212
2 types of cooperativity
pos and neg
213
positive cooperativity
binding of a substrate to one subunits increases the affinity of the other subunits
tense → relaxed
214
negative cooperativity
binding of a substrate to a subunit reduces the affinity of other subunits
215
distinction between allosteric binding and cooperativity binding
cooperativity binding occurs at the active site
allosteric occurs at other sites
216
competitive inhibitors
inhibitors that compete with substrate for binding at the active site
can be overcome by adding more substrate (outcompete)
Km is increased with competitive inhibitors
217
noncompetitive inhibitors
bind at the allosteric site, not active
adding more substrate won't help
lowers Vmax
doesn't usually alter Km
substrate still binds but catalytic activity is prevented
218
uncompetitive inhibitors
inhibitors that can only bind after the enzyme-substrate complex has formed
bind to allosteric sites
decreases Vmax
decreases Kmax
219
what is Km
conc. of substrate that allows for the enzyme to reach half Vmax
lower Km = higher affinity
220
mixed-type inhibition
inhibitor can bind to either the unoccupied enzyme OR the enzyme-substrate complex
221
when does Km increase for mixed-type
if the enzyme has a greater affinity for in its free form → lower affinity for the substrate
similar to competitive inhibition
222
when does Km decrease for mixed-type
if the enzyme-substrate complex has a greater affinity for the inhibitor → greater affinity
similar to uncompetitive inhibitor
223
mixed type - equal affinity
it would be a non-competitive inhibitor
224
Lineweaver-Burk plot
225
slope of L-B plot
Km / Vmax
226
y intercept of L-B plot
1 / Vmax
227
x intercept of L-B plot
-1 / Km
228
competitive inhibitors..
do not affect Vmax but increase Km
229
noncompetitive inhibitors..
decrease Vmax but don't change Km
230
uncompetitive inhibitors..
reduce Km and Vmax
231
mixed type inhibitors..
reduce Vmax but have variable effects on Km
232
do catalysts affect thermodynamics
no, only kinetics
233
characteristics of enzymes (3)
increases the rate of reaction
cannot be used up
specific for a specific reaction
234
where do substrates bind
active site
235
easiest way to turn an enzyme on/off
phosphorylation
236
2nd most common way to regulate enzyme activity
allosteric regulation
237
purpose of pos feedback
drives a reaction to a certain end point
e.g. contractions → birth
238
Vmax depends on..
enzymes!
the specific enzyme & enzyme conc.
239
decreased Km..
increased enzyme affinity for substrate
240
all biologically produced amino acids have ___ configuration
L
241
which AA plays a central role in the formation of alpha helices and beta sheets
proline
