Biochemistry Class 1 Flashcards
(182 cards)
1
Q
substrate binds to what type of macromolecule
A
enzyme
2
Q
an enzyme is said to be saturated when _______ (2 facts)
A
- so much substrate is attached to all active sites that they are continuously occupied
- adding more substrate does not increase the reaction rate
3
Q
enzyme saturation is denoted by what symbol?
A
Vmax
4
Q
how do we know the Vmax of each enzyme?
A
Vmax is a property of each enzyme at a particular concentration of enzyme.
5
Q
reaction rate for enzyme kinetics is ______ (def + fact)
A
- amount of product formed per unit time in mole per second (mol/s).
- determined by concentration of substrate and enzyme
6
Q
allosteric regulation (2 facts)
A
- binding of small non-substrate molecules to particular sites on enzyme other than the active site
- alters the conformation of the active site of the enzyme in such a way that the catalysis is increased or decreased binding is reversible and non-covalent
7
Q
What does the V vs [S] graph (enzyme kinetics) show and what does each letter mean
A
how the reaction rate varies according to substrate concentration V= velocity (Rate of reaction) where Vmax is upper limit [S] = substrate concentration
8
Q
what is Km in enzyme kinematics
A
a constant for a given enzyme/substrate combo that is the measure of substrate concentration at 1/2 Vmax.
9
Q
low Km means: ____low/high?_____ affinity of enzyme for the particular substrate
A
high
<em>MCAT trick!</em>
10
Q
T/F: Vmax is constant for a given enzyme/substrate pairing
A
True
11
Q
competitive inhibitor binds at ________site
A
active
12
Q
in enzyme kinetics, the sigmoidal curve represents__________.
What’s an example?
A
positive cooperative binding
Oxy-hemoglobin dissociation curve
13
Q
What is positive cooperative binding? (2 facts)
A
- When the binding of substrate to one subunit increases the affinity of other subunits for substrate.
- conformation of enzyme is said to be tense at low concentration of [S] → low affinity and relaxed at high concentrations → high affinity
14
Q
T/F: You cannot get to Vmax with presence of competitive inhibitor
A
False: You can, it just takes longer and requires more substrate
15
Q
presence of a competitive inhibitor ____increases/decreases?_____ Km
A
increases
16
Q
A
17
Q
what effect on Km does non-competitive inhibitor have
A
it does not change it because binding of an inhibitor at allosteric site does not increase or decrease affinity, which alters Km
18
Q
[S]surroundings + [S]system = [S]universe
is [S] greater or less than zero
A
[S]surroundings + [S]system = [S]universe >0
19
Q
If ΔH and T constant…
then when ΔS is positive, what is ΔG?
A
ΔG is negative
ΔS positive means that the entropy of the universe [S]final increased as a result of the reaction, and the 2nd law of thermodynamics states that this occurs in spontaneous reactions, which is denoted by -ΔG
20
Q
T/F We can transform endergonic reactions to exergonic reactions by increasing the concentration of reactants
A
True
21
Q
When ΔG = 0, the reaction is _______
A
at equilibrium
22
Q
What is the gas constant, R
A
8.314 J/mol · K
23
Q
how do you convert C° to K
A
add 273 to your temp in C°
24
Q
What are 2 mathematical ways to determine whether the reaction will favor products or reactants and to what extent?
A
- Look at ΔG: if -ΔG then reaction favors products and the magnitude of the value is proportional to the magnitude of the drive to make products
- Look at whether Q (conc. of products/reactants) is > or < Keq. If Q<k>eq then reaction is drive to the right (towards products) in an effor to reestablish equilibrium. Again, the extent to which Q<k>eq indicates how much drive it has</k></k>
25
endergonic vs exergonic
endergonic: reaction requires energy to take place; is non-spontaneous
exergonic: reaction is spontaneous and the system loses energy to the surroundings.
26
a spontaneous reaction
is \_\_\_\_\_\_\_\_\_\_\_-ically favorable
thermodynamically favorable
27
What 2 outcomes does a catalyist acheive in the kinematics of a reaction?
1. Decrease activation energy Ea
2. Stabilizes transition state TS
28
T/F a catalyst lowers the ΔG of a reaction
FALSE it does not change ΔG
29
chemoheterotroph
an organism that uses the energy of checmicals produced by other living things (humans)
30
How is chemical energy converted into useable energy?
Plants and animals store chemical energy in reduced molecules such as carbohydrates and fats. These reduced molecules are oxidized to produce CO2 and ATP. ATP is used to drive energetically unfavorable reactions of the cell
\*This is why oxygen is vital to the survival of all living tissues
31
Oxidation (can mean 3 things)
1. gain of oxygen
2. loss of hydrogen
3. loss of electrons
32
Reduction (can mean 3 things)
1. loss of oxygen
2. gain of hydrogen
3. gain of electrons
33
Is changing Fe3+ to Fe2+ oxidation or reduction?
reduction
mnemonic: just compare whatever chemical event is occuring with loss or gain of oxygen. If it's opposite (loss is opposite of gain), then they're in the same group.
34
redox pair
whenever one molecule is reduced, another must be oxidized and visa versa: These 2 molecules participate in a redox pair
35
catabolism
process of breaking down molecules
e.g. "oxidative catabolism" is breaking down glucose for energy
36
breaking down glucose for energy is an example of \_\_\_\_\_\_\_\_\_-bolism
catabolism
37
anabolism
process of building up metabolism
e.g. using ATP to generate molecules such a glycogen and fatty acids via reduction
38
anabolic processes are typically \_\_\_\_\_\_\_\_-ive
reductive
39
A Bronsted-Lowry acid is a H+ \_\_\_\_\_\_\_\_\_\_\_
A lewis acid is an electron pair \_\_\_\_\_\_\_\_\_\_\_
H+ donor
electron pair acceptor
40
Ka = ?/?
products / reactants
e.g. for a generic acid HA in water, the Ka would be [H3O+][A-]/HA
called the **acid dissociation constant** (of HA for example) and measures how much products are favored over reactants i.e how strong the acid is
41
higher Ka means \_\_\_\__stronger/weaker?_\_\_\_ acid
higher Ka means **_stronger_** acid
e.g. given product/reactants = 3/2 ..shows mathematically that more of the product (numerator, 3) is being made. 3/2 is higher Ka than 2/3
42
polyprotic acid
an acid that has more than 1 proton that can be donated (ie ionizable proton)
e.g. H2CO3
43
a molecule is said to be amphoteric when \_\_\_\_\_\_\_\_
it can act as an acid or base
e.g. amino acid
44
in water, since, [H+][OH-]=10-14
we can derive the equation:
pH + pOH = 14
45
in general, the "p" of something equals the -log of that something
true
46
the higher the pKa, the _________ the acid
weaker
47
buffer definition
a buffer is a solution that resists changing pH when a small amount of acid or base is added.
48
buffering capacity is greatest when
the presence of a ***_weak_*** acid and its conjugate base are in equal concentrations
49
C because the total amount of product formed once the reaction has reaced equilibium is determined by thermodynamic factors, whereas the amount of product formed in a given time period is determined by kinetic factors
50
what characteristic of the peptide bond is responsible for a rigid primary structure? (no rotation about a single bond)
resonance, which creates a partial double bond of th peptide bond
51
what does the secondary structure of proteins look like and what characterizes them?
either alpha helix or beta pleated sheet
both are made up of repeating motifs and are characterized by H bonding
you will not find proline in an A-helix
52
Tertiary structure is d/t \_\_\_\_\_\_\_\_interactions within a polypeptide
side chain
53
Types of interactions that can make up tertiary structure
Non-Covalent
1. Polar/polar, nonpolar/nonpolar
2. electrostatic
3. acid/base
Covalent
1. disulfide bridges
54
does a protein have to have all 4 levels of structure to be functional
no, but has up to tertiary
55
Quarternary structure occurs d/t
side chain interactions between different polypeptides
56
Definition of cofactor
A cofactor is a nonorganic molecule whose presence is necessary for the proper function of an enzyme.
57
T/F: Entropy, enthalpy, and free energy are all thermodynamic quantities.
True
they cannot be considered when analyzing the catalytic effect of two different enzymes on a chemical reaction. (that's kinetics)
58
T/F: Denaturation of an enzyme will alter the kinetics of a reaction that it catalyzes.
True
59
T/F: The kinetics of a reaction can be characterized by a rate-constant
True
60
The induced fit model of enzyme binding states that the ___________ alters the enzyme active site to more closely match the shape of the substrate.
the substrate itself
An enzyme and a substrate must come into close physical proximity for binding to occur, and such proximity can introduce physical forces that alter the shape of the enzyme.
61
The lock and key model states that \_\_\_\_\_
the active site of an enzyme matches the binding site of the substrate, which explains the specificity of enzymes for certain substrates
62
A \_\_\_\_\_catalyzes the formation of a single bond between two substrates through the elimination of water.
ligase
63
T/F: Catalysts make reactions fast by aligning reactants so that successful reactions are more likely!
True
64
An enzyme not bound to its cofactor is called
Apoenzyme
65
An enzyme bound to its cofactor is called
haloenzyme
66
disulfide bonds are found in \_\_\__intracellular/extracellular_\_\_\_\_\_ polypeptides
extracellular, because inside the cell is a reducing environment
e.g. insulin, antibodies
67
Phosphoglucomutase, which catalyses the formation of glucose-6-phosphate from glucose-1-phosphate, is best classified as which enzyme type?
isomerase, because glucose-6-phosphate is an isomer of glucose-1-phosphate.
Enzymes are classified according to the sort of reaction they catalyze.
68
T/F: Enzymes can increase the rate of reactions that have a positive
FALSE
only reaction coupling can assist with this
69
What are oxidoredutases?
“catalyze oxidation–reduction reactions that involve the transfer of electrons.” Movement of hydride is key to identifying REDOX reactions.
includes oxidases, reductases, dehydrogenases
70
What are transferases?
“move a functional group from one molecule to another molecule.”
Kinase is an example of a transferase moving phosphate groups.
71
What do hydrolases do?
“ catalyze cleavage with the addition of water.”
Most catabolic metabolism in the body is due to hydrolases.
72
What are lyases?
Catalyze cleavage by means other than oxidation or hydrolysis reduction. The reverse reaction (synthesis) is often more important biologically.
73
What are isomerases?
“ catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers.”
74
What are ligases?
“are responsible for joining two large biomolecules, often of the same type, by forming a chemical bond, often of the same type.” REQUIRE ATP, seen in genetics during dna replication.
75
Mnemonic for enzyme classifications?
LILHOT
Ligase, Isomerase, Lyase, Hydrolase, Oxidoreductase, Transferase.
76
Why is the statement "An increase in the substrate concentration leads to proportional increases in the rate of the reaction" false?
As the reaction initially beings, this statement is true. Once the reaction hits Vmax, this statement stops being true.
77
What are some characteristics of an enzyme?
1. Lower the activation energy
2. Increase the rate of the reaction
3. Does not alter the equilibrium constant
4. Are not changed or consumed in the reaction (which means that they will appear in both the reactants and products.)
4. Are pH- and temperature-sensitive, with optimal activity at specific pH ranges and temperatures
5. Do not affect the overall ΔG of the reaction
6. Are specific for a particular reaction or class of reactions”
78
What are Kinases
enzymes that transfer a phosphate group to a molecule from a high energy carrier such as ATP (e.g. phosphofruktokinase)
this is a transferase
79
What are polymerases?
catalyzes polymerization
e.g. addition of nucleotides to the leading strand of DNA by DNA polymerase III
80
Phosphetase
removes a phosphate group from a molecule
81
protease
hydrolyzes peptide bonds
e.g. trypsin, chymotrypsin, pepsin
82
in ____________ a favorable reaction is used to drive an unfavorable one
reaction coupling
83
cofactors are \_\_\_\__inorganic/organic_\_\_\_ molecules
inorganic
84
What's physical properties of the active site allow it to function?
they contain catalytic resides of AAs that are responsible for lowering the transition state
85
What are the strategies/mechanisms by which enzymes do their job?
1. Active sites contain microenvironments
* they typically contain non-polar environment in which bonds can be formed and broken very easily
* will not contain H20 unless water is actively involved in the catalytic activity
2. Active sites bind substrates reversibly in non-covalent interactions
* In order to have meaningful non-covalent interactions, the distance between substrate and the residues of the active site must be short enough, which is why active sites have structures complementary to their corresponding substrate---\> explained by lock and key model vs induced fit model
86
Describe the induced fit model
The actice site is not perfectly complementary to the substrate, but it conforms to the substrate after binding.
ie. An enzyme and a substrate must come into close physical proximity for binding to occur, and such proximity can introduce physical forces that alter the shape of the enzyme.
87
If the enzyme-catalyzed reaction E + S ⇋ ES ⇋ E + P is proceeding at or near the Vmax of E, what can be deduced about the relative concentrations of S and ES?
Choose 1 answer:
[S] is vanishingly low, [ES] is vanishingly low
S is abundant, [ES] is at its highest point
S is abundant, [ES] is vanishingly low
[S] is vanishingly low, [ES] is at its highest point
**S is abundant, [ES] is at its highest point**
At Vmax, the enzyme is fully saturated, and no more free enzyme is available to bind the substrate and catalyze the reaction.
If all of the enzyme, E, is bound and operating, it must all exist in the ES state.
In order to maintain Vmax there must be sufficient substrate for the enzyme to bind, so [S] must be high enough to sustain this saturated state.
88
the magnitude of Km depends on
environment and substrate concentration
89
when [S] = Km then how many active sites are bound?
exactly 1/2
which also means that [ES] = [E]total / 2
it also means that Vnot=Vmax/2
90
when [E][S] \>\> [ES] which is represented by [E][S]/[ES] then that means the unbound species is much greater than the bound. What can we conclude about the binding affinity between enzyme and substrate?
There is low affinity
91
when the K-1 is \>\>\> greater than k2 the Michaelis constant Km describes
the likelihood of dissociation of the enzyme-substrate complex.
92
a competitive inhibitor acts by:
having a higher affinity for the active site than the substrate itself has.
\*however, if you increase the concentration of the substrate, then there is a higher chance of the substrate bumping into the active site and outcompeting the inhibitor
93
why is Vmax unaffected in the case of a competitive inhibitor?
because it is possible to add enough substrate to outcompete the inhibitor, which will yield the same Vmax as before
\*this has to increase Km, which is the substrate concentration required to get to 1/2 Vmax
94
you have an enzyme-inhibitor complex. Adding more substrate allows you to reach Vmax eventually. what's the type of inhibitor
competitive
95
how does the graph for a competitive inhibitor differ from that of a non-competitive inhibitor?
96
How does uncompetitive inhibition work?
The binding of the substrate creates a confomational change, which creates a new allosteric site. The inhibitor binds to this new allosteric site, creating an enzyme-substrate-inhibitor complex. Once it binds, it blocks the acitivity of the enzyme by increasing the apparent affinity of the substrate to the enzyme, making it unable to readily dissociate
97
\_\_\_\_\_\_\_\_\_\_\_inhibitors operate on enzymes have a permament allosteric site where the inhibitor binds to and can bind there whether or not the substrate is bound. If inhibitor is bound, no product will be made.
non-competitive
98
How does non-competitive inhibition work?
noncompetitive inhibitors bind at a permanent allosteric site and prevent the catalytic activity of enzymes from afar. The inhibitor does not increase the affinity at active site, so Km is unaffected. Since catalytic velocity is reduced permamently, Vmax is decreased
mnemonic:
NON=NOt Near (in reference to the allosteric site)
and NON = NO change (to Km)
99
list the mechanisms of enzymatic control
1. Allosteric Control
* observes cooperativity: binding of molecule affects affinity of other sites for that same molecule
2. Reversible covalent modification
* most common: addition of phosphoryl group onto the enzyme from ATP. this phsophoryl group activates or inactivates the acitivty of the enzyme. Protein kinase does the transfer.
3. Proteolytic Cleavage
* many enzymes are produced in inactive form called "zymogen" or "proenzymes". Proteases cleave at special sites to activate the enzyme.
4. Association with other polypeptides
* some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit.
100
What are the parts to a lineweaver burk plot and what's its function?
as Vmax decreases, the y intercept is moved up, as Km decreases, the x intercept is moved to the right
it functions to visually identify inhibitor type and it allows us to calculate Vmax if you're given a y intercept and to calculate Km if you're given a y intercept
101
What does the lineweaver burk plot look like for a competitive inhibitor
102
What does the lineweaver burk plot look like for a uncompetitive inhibitor?
103
What does the lineweaver burk plot look like for a noncompetitive inhibitor?
104
Cooperative enzymes must have:
1. exactly one active site
2. more than one
More than one
\*this also means that they are likely to be multisubunit complexes
105
T/F: increasing the temperature of an enzyme's surroundings may or may not affect the likelihood of an enzyme binding its substrate
True.
UNLESS the temperature is increased to the point of denaturing
106
Km is can be used to measure binding affinity. because Km = [E][S]/[ES], so as Km increases, binding affinity \_\_\_\_\_\_\_\_\_\_
decreases
107
On a lineweaver-Burk plot, as Vmax decreases, the y intercept ________ (because y-intercept is 1/Vmax)
increases
108
DNA methylation occurs via addition of a methyl group to \_\_\_\_\_\_\_
cytosine, resulting in methyl-cytosine base-pairing with guanine.
109
In which of the following situations would there be the greatest yield of products at equilibrium following the addition of an enzyme?
1. A reaction favoring reactants and small activation energy.
2. A reaction with less stable reactants and large activation energy.
3. A reaction with more stable reactants and small activation energy.
4. A reaction favoring reactants and large activation energy.
A reaction with less stable reactants and large activation energy.
The greater the stability of the reactants, the more they are favored at equilibrium and the greater the stability of products, the more they are favored at equilibrium. Therefore the reaction with less stable reactants would favor products at equilibrium and generate a greater yield.
110
T/F: increasing substrate concentration does not have an effect on Km of an enzyme?
true
111
112
What interactions maintain each type of protein structure?
1. Primary structure is the sequence of amino acids linked by peptide bonds
2. Secondary structure is maintained primarily by hydrogen bonds.
3. The bonds/interactions responsible for maintaining quaternary structure of a protein are the same bonds/interactions responsible for the tertiary structure: interaction of protein subunits, maintained by both **intermolecular forces** and **disulfide bridges**
113
Which of the following is NOT a function of cholesterol?
1. Energy storage
2. Precursor for bile
3. Precursor for steroid hormones
4. Increase fluidity of plasma membranes
Energy storage
114
T/F: reaction rate is independent of enzyme concentration.
FALSE:
Doubling the amount of enzyme doubles the number of available active sites, and so doubles the rate of the reaction. The addition of more active sites (without the addition of more substrate) will not lead to saturation, in fact it is the opposite. Reaction rate is clearly dependent on enzyme concentration; initially, at an enzyme concentration of zero, the reaction rate was stated to be “very slow”. When enzyme was added, the reaction rate doubled. Enzymes have no effect on the equilibrium constant. They do not change the equilibrium point of a reaction, they only speed up the rate at which the reaction reaches equilibrium.
115
Feedback inhibition involves the decrease in activity of an enzyme by \_\_\_\_\_\_\_\_\_
binding to a downstream product.
116
an anti-substrate antibody binds to \_\_\_\_\_\_\_
the substrate
117
does Vmax depend on substrate concentration?
NO
from the pic.. III. is wrong because its another way of saying competitive inhibition, which doesn't change Vmax
118
enzyme concentration always affects Vmax
119
what is a zymogen
an inactive enzyme that requires a covalent modification
120
define coenzyme
organic nonprotein molecules that bind with the protein molecule (apoenzyme) to form the active enzyme (holoenzyme).
121
what's the difference between a coenzyme and a cofactor?
a coenzyme is involved in helping catalysis
a cofactors participate in enzymatic activity
122
what process serves as the principle energy source for cellular metabolism?
oxidation of carbohydrates (aka combustion)
123
a glycosidic linkage is
a link between two monosaccharides
a covalent bond that forms in dehydration reaction
named according to which carbon is involved in the bond: alpha or beta
124
humans can't digest which glycosidic linkage? what's the exception
beta
with the exception of lactose.
125
what's the chemcial formula for a monosaccharide?
Cn H20n
smallest functional monosaccharide is n=3
126
How do you determine the steriochemistry of monosaccharides?
find the chiral carbon farthest from the aldehyde or ketone group (pictured at top of molecule in Fischer diagrams) and note whether it's OH group falls to the right or the left
if R=D
if L=L
127
define epimer
a specific type of diateriomers that differ at only one carbon configuration
128
How do you convert between a noncyclic monosacharide and its cyclic counterpart (present in equal amounts)
make the O from the priority OH group attack the C=O group \> what was the carbonyl carbon is our 1 carbon in the cyclic structure but in the cyclic structure the carbonyl group is now an OH group. orient the other groups as follows: right groups down and the left groups up and the CH2OH group at the bottom up
see next card for config of -OH group
129
how doy ou decide the configuration of the anomeric OH group in cyclic sugar structures in chair conformation?
anomer = the OH group attached to C1
The -OH group off our 1 carbon is beta if its oriented cis with respect to the last carbon in the ring and alpha if it's oriented trans from it
130
The epimers of glucose are
mannose and galactose
131
sucrose is a mono or disacharide?
Sucrose is a disaccharide of fructose and glucose.
132
define anomer
Anomers are epimers that are in their cyclic state.
133
A furanose is a _____ membered ring featuring \_\_\_\_\_\_\_carbons and one oxygen.
five
4 carbons
134
A pyranose is a _____ membered ring featuring \_\_\_\_\_\_\_carbons and one oxygen.
6
5 carbons
135
The straight chain form of glucose differs from the straight chain form of fructose in which way?
Type of carbonyl functional group
136
Cleavage of two unknown disaccharides is shown by infrared spectroscopy to result in 4 individual monosaccharide molecules, 2 with ketone functionality, and 2 with aldehyde functionality. Based on this data, what is the identity of the two unknowns?
1. Lactose, maltose
2. Sucrose, sucrose
3. Lactose, sucrose
4. Maltose, maltose
Answer: Sucrose, sucrose
Hint #11 / 4
Lactose is a disaccharide of glucose and galactose. Both of these have aldehyde functionality.
Hint #22 / 4
Maltose is a disaccharide of glucose and glucose.
Hint #33 / 4
Sucrose is a disaccharide of glucose and fructose. Fructose is the a monosaccharide with ketone functionality.
Hint #44 / 4
Based on the data, the identity of the two unknowns is sucrose and sucrose. This will create two molecules of fructose (ketone functionality) and two molecules of glucose (aldehyde functionality).
137
T/F:A glycosidic bond connects an anomeric carbon of one sugar to an alcohol oxygen of another sugar.
true
138
T/F D-sugars have the same absolute configuration at the asymmetric center farthest from their carbonyl group as does D-glyceraldehyde.
True
139
all D-Aldohexoses are diasteriomers of one another
true
140
The chiral carbon furthest from the carbonyl group determines the absolute configuration of the sugar.
True: it tells you L or D, which is the absolute configuration
141
The presence of the following structural features of this molecule most likely accounts for a molecules inability to cross the blood-brain barrier?
A. An aromatic ring
B. A carbonyl group
C. A quaternary ammonium
D. A tertiary amine
Small, hydrophobic molecules pass easily through the blood-brain barrier, while charged and larger molecules have difficulty doing so. An aromatic ring is highly hydrophobic and thus would have no difficulty passing through the barrier (choice A is eliminated). While the neostigmine molecule does both have a carbonyl group and a tertiary amine, polar groups which would hinder passing through the hydrophobic barrier, the quaternary ammonium cation is actually charged and thus is the main problem in crossing the barrier (choices B and D are eliminated, choice C is correct).
142
Competitive Inhibition
binds at ?
effect on Vmax?
effect on Km?
143
Uncompetitive Inhibitor:
binds at?
effect on Vmax?
effect on Km?
144
Mixed inhibition
binds at?
effect on Vmax
effect on Km?
145
What is the Gibbs free energy equation and what do each of the terms mean?
146
T/F: delta G can tell you how fast a reaction will occur
false, only kinematics can tell you that. it only tells you whether a reaction is spontaneous
147
all the macromolecules for the MCAT are \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_. Enzymes that make them are called \_\_\_\_\_\_\_\_\_\_\_. Reactions that make them are called ____________ reactions
All the macromolecules for the MCAT are **Polymers** Enzymes that make them are called **polymerases**. Reactions that make them are called **polymerization** reactions (aka condensation or dehydration synthesis)
148
What's a lipid made out of
it's made out of a long unsubstituted hydrocarbon chain (the monomer) with a carboxlic acid at the end.
a lipid is either saturated or unsaturated (referring to the hydrogen saturation)
149
what's the difference between saturated and unaturated lipids/fats
**Saturated**: there is no double bond in the lipid molecule, making it able to conense at room temperature because it can arrange in tight stacks (e.g. lard, butter, etc)
**Unsaturated:** there is a double bond within the hydrocarbon chain, so the shape is less regular and it cannot arrange in a stack as easily and it will not be solid at room temp (still stable though) e.g. olive and other oils
150
What are the forms of fatty acids in the body?
1. Triglyceride
2. Phospholipids
3. terpenes
4. cholesterol
151
Describe a triglyceride?
a fatty acid comprised of 3 saturated lipid chains (either the same or different, usually 14-18 carbons long, made with even numbers of Cs in the body) joined together by glycerol at the carboxylic acid terminus (via dehydration synthesis).
The storage form of fatty acid is fat and "triglyceride" is the technical term for fat.
Because they are saturated and have consistent structures, they can create stacks and layer up, which is why they are condense solids at room temp
152
Describe a phospholipid aka phosphatides
2 lipid chains attached by a glycerol molecule except instead of a 3rd fatty acid chain (like in triglyceride) you have a phosphate group at one end. This provides the polar head. Phospholipids are derived from DG-P and will spontaneously form a lipid bilayer
also used as surfactant
because of the double bond, they cannot form stacks and are not solids at room temp, this also makes them better as a lipid bilayer, so that there remains membrane fluidity by preventing membrane solidification through packing
153
Describe a terpene
lipid made from at least 2 isoprene units strung together. Terpenes are named after the number of double isoprene units there are. May be cyclic or linear
e.g. squalene has 6 units, which makes it a triterpene. (3 sets of 2 isoprenes)
Functions: precursor of cholesterol, ear wax, steroids
can be modified to create terpenoid
154
describe cholesterol
a steroid made up of 3 6-carbon rings and 1 5-carbon ring. any derivative of cholesterol will have these rings. it is obtained from diet and synthesized in the liver. it is carried in the blood packaged with fats and proteins - called lipoproteins
Functions: to serve as precursor for:
* hyrophobic steroid hormones
* Vitamin D
* bile salts
* cell membrane - serves to keep membrane fluidity at optimal level
155
what would happen if you subjected your triglycerol to saponification
it would undergo base catalyzed hydrolysis into fatty acid salts plus glycerol
156
who stores more energy content, carbohydrates or fats?
fats, because they are much more reduced/less oxidized. This means that since using up energy starts with oxidation, having a starting molecules that is primed for oxidation rather than already oxidized results in more energy.
157
what are the structural determinants of membrane fluidity?
degree of saturation, tail length, amount of cholesterol
158
what does an isporene unit look like?
has chemical formula C5H8
159
what are sphingolipids
lipids that are structured similarly to phospholipids, but instead of glycerol as the backbone, sphingosine is the backbone.
picture attached is of a sphingomyelin, an important component of the myelin sheath around neurons
160
what are waxes?
long chain fats esterified to long chain alcohols.
They are so hydrophobic that they form waterproof barriers in plants and earwax
161
what defines the structure of a steroid?
having the same core tetracyclic ring system as cholesterol.
They are hydrophobic
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How do steroid hormones act on the body?
Their hydrophobicity allows them to diffuse through the lipid bilayer membrane into the cytoplasm. there are no receptors for steroid hormons on the surface of cells, rather, the receptors are within the cell.
## Footnote
*\*MCAT trick: don't confuse steroid hormone with peptide hormones espeically in terms of receptor location*
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What are the steroid hormones?
testosterone, estrogen, progesterone, aldosterone, cortisol
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what's the main difference between steroid hormones and peptide hormones?
**Peptide hormones** exert their effects by binding to receotprs at the cell-surface.
**steroid hormones** diffuse into cells to find their receptors
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what are the peptide hormones?
insulin, glucagon, somatostatin, melatonin, erythropoetin, thrombopoetin, ANP, Thymosin
(not a complete list)
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what are the fat soluble vitamins and what structure do they have in common?
Vitamins A, E, D3, K
mnemonic: get me the AED stat, K?!
all have ring structures
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Prostaglandins
derived from 20-carbon fatty acids
they have different roles in different tissues depending on the receptor they bind. they regulate:
* smooth muscle contraction in intestines and uterus
* blood vessel dilation
* gastric integrity by decreasing acid secretion and increasing mucus in the stomach
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substrate analog
molecules (usually inhibitors) that have a similar structure to the substrate
in competitive inhibition, this allows them to covalently bind to the active site of the enzyme.
In uncompetitive inhibition, the inhibitor may resemble the substrate but it binds at a location separate from the active site
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what would be the most likely class of inhibitors that a substrate analog would belong too
competitive: because they need a property that allows them to take over/bind to the active site.
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Mechanisms of direct enzymatic regulation?
1. Removal of a phosphate with the use of a phosphatase
2. Peptide hydrolysis
3. Interaction of the enzyme with downstream products
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how are dietary fats broken down?
Due to the activity of lipase, triglycerides are broken down into two fatty acids and a monoglyceride before absorption and ultimate reassembly into a triglyceride in the enterocyte.
Note that triglycerides are dietary fat, which are also known as triacylglycerol.
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definition of denaturing
disruption of a proteins shape without breaking peptide bonds
e.g. misfolding
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what drives the folding of secondary structures such as alpha helixes into higher order tertiary structures?
interactions of R groups with each other and with the solvent
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which of the following may be considered an example of tertiary protein structure formation
1. van der Waals forces
2. Hydrogen bonds between backbone and amino and carboxyl groups
3. Covalent disulfide bonds between cysteine residues located far apart on a polypeptide
Van der Waals and Covalent disulfide bonds
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quaternary structure
interactions between polypeptide subunits ie a multisubunit complex. peptide bonds do not contribute to quaternary structure, this belongs to primary
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carbohydrates can be broken down into CO2 in a process called \_\_\_\_\_\_\_
oxidation
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What is pyrophsophate and how does its structure contribute to in being such a good energy source?
pyrophosphate is a structure composed of 2 orthophosphates (aka phosphates) bound together via an anhydride linkage. The POP bond in pyrophosphate is an example of a high-energy phosphate bond for 3 reasons:
1. when phosphates are linked together their negative charges repel eachother strongly
2. when separated, they have more responsnce forms and thus lower energy, so it's breakage is favorable
3. orthophosphate has more favorable interaction with the biological solvent water than linked linked phosphates
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what does a single unit of phosphoric acid vs phosphate look like?
phosphoric acid has 1 or more hydrogens still associated. At physiological pH, it becomes deprotonated, earning the name phosphate, or inorganic phosphate Pi (when unattached to organic matter)
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does starch have alpha or beta glycopsidic linkages?
alpha (basically same as glycogen)
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Which statement best describes how cholesterol affects cell membrane fluidity?
A) Decreases fluidity @ low temps, increases fluidity @ high temps
B) Increases fluidity @ low temps, decreases fluidity @ high temps
C) Decreases fluidity @ low temps, decreases fluidity @ high temps
D) Increases fluidity @ low temps, increases fluidity @ high temps
B) Increases fluidity @ low temps, decreases fluidity @ high temps
- The fluidity of cell membranes is determined in large part by how well the fatty acid tails of phospholipids can interact with each other via Van der Waals forces. The closer fatty acids can pack together the LESS fluid the membrane becomes.
- At high temperatures, phospholipids are already fairly well-separated from each other. Cholesterol fills in these gaps, pulling phospholipids closer together & increases strength of Van der Waals forces among fatty acid tails.
- Cholesterol decreases fluidity at high temperatures (due to increased Van der Waals forces) and increases fluidity at low temperatures (due to decreased Van der Waals forces).
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During the formation of a disaccharide, the \_\_\_\_\_\_\_\_\_\_group of one monosaccharide reacts with the _________ group of a second monosaccharide to form a glycosidic linkage.
During the formation of a disaccharide, the hemiacetyl group of one monosaccharide reacts with the hydroxyl group of a second monosaccharide to form a glycosidic linkage.
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