Biochemistry Class 1

Question 1

substrate binds to what type of macromolecule

Answer 1

enzyme

Question 2

an enzyme is said to be saturated when _______ (2 facts)

Answer 2

1. so much substrate is attached to all active sites that they are continuously occupied
2. adding more substrate does not increase the reaction rate

Question 3

enzyme saturation is denoted by what symbol?

Answer 3

V_max

Question 4

how do we know the V_max of each enzyme?

Answer 4

Vmax is a property of each enzyme at a particular concentration of enzyme.

Question 5

reaction rate for enzyme kinetics is ______ (def + fact)

Answer 5

1. amount of product formed per unit time in mole per second (mol/s).
2. determined by concentration of substrate and enzyme

Question 6

allosteric regulation (2 facts)

Answer 6

1. binding of small non-substrate molecules to particular sites on enzyme other than the active site
2. 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

Question 7

What does the V vs [S] graph (enzyme kinetics) show and what does each letter mean

Answer 7

how the reaction rate varies according to substrate concentration V= velocity (Rate of reaction) where Vmax is upper limit [S] = substrate concentration

Question 8

what is K_m in enzyme kinematics

Answer 8

a constant for a given enzyme/substrate combo that is the measure of substrate concentration at 1/2 Vmax.

Question 9

low K_m means: ____low/high?_____ affinity of enzyme for the particular substrate

Answer 9

high

_{<em>MCAT trick!</em>}

Question 10

T/F: Vmax is constant for a given enzyme/substrate pairing

Answer 10

True

Question 11

competitive inhibitor binds at ________site

Answer 11

active

Question 12

in enzyme kinetics, the sigmoidal curve represents__________.

What’s an example?

Answer 12

positive cooperative binding

Oxy-hemoglobin dissociation curve

Question 13

What is positive cooperative binding? (2 facts)

Answer 13

1. When the binding of substrate to one subunit increases the affinity of other subunits for substrate.
2. conformation of enzyme is said to be tense at low concentration of [S] → low affinity and relaxed at high concentrations → high affinity

Question 14

T/F: You cannot get to Vmax with presence of competitive inhibitor

Answer 14

False: You can, it just takes longer and requires more substrate

Question 15

presence of a competitive inhibitor ____increases/decreases?_____ K_m

Answer 15

increases

Question 16

Answer 16

Question 17

what effect on K_m does non-competitive inhibitor have

Answer 17

it does not change it because binding of an inhibitor at allosteric site does not increase or decrease affinity, which alters K_m

Question 18

[S]_surroundings + [S]_system = [S]_universe

is [S] greater or less than zero

Answer 18

[S]_surroundings + [S]_system = [S]_universe >0

Question 19

If ΔH and T constant…

then when ΔS is positive, what is ΔG?

Answer 19

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

Question 20

T/F We can transform endergonic reactions to exergonic reactions by increasing the concentration of reactants

Answer 20

True

Question 21

When ΔG = 0, the reaction is _______

Answer 21

at equilibrium

Question 22

What is the gas constant, R

Answer 22

8.314 J/mol · K

Question 23

how do you convert C° to K

Answer 23

add 273 to your temp in C°

Question 24

What are 2 mathematical ways to determine whether the reaction will favor products or reactants and to what extent?

Answer 24

1. 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
2. Look at whether Q (conc. of products/reactants) is > or < K_eq. 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>

Question 25

endergonic vs exergonic

Answer 25

endergonic: reaction requires energy to take place; is non-spontaneous
exergonic: reaction is spontaneous and the system loses energy to the surroundings.

Question 26

a spontaneous reaction

is ___________-ically favorable

Answer 26

thermodynamically favorable

Question 27

What 2 outcomes does a catalyist acheive in the kinematics of a reaction?

Answer 27

1. Decrease activation energy Ea
2. Stabilizes transition state TS

Question 28

T/F a catalyst lowers the ΔG of a reaction

Answer 28

FALSE it does not change ΔG

Question 29

chemoheterotroph

Answer 29

an organism that uses the energy of checmicals produced by other living things (humans)

Question 30

How is chemical energy converted into useable energy?

Answer 30

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

Question 31

Oxidation (can mean 3 things)

Answer 31

1. gain of oxygen
2. loss of hydrogen
3. loss of electrons

Question 32

Reduction (can mean 3 things)

Answer 32

1. loss of oxygen
2. gain of hydrogen
3. gain of electrons

Question 33

Is changing Fe³⁺ to Fe²⁺ oxidation or reduction?

Answer 33

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.

Question 34

redox pair

Answer 34

whenever one molecule is reduced, another must be oxidized and visa versa: These 2 molecules participate in a redox pair

Question 35

catabolism

Answer 35

process of breaking down molecules

e.g. “oxidative catabolism” is breaking down glucose for energy

Question 36

breaking down glucose for energy is an example of _________-bolism

Answer 36

catabolism

Question 37

anabolism

Answer 37

process of building up metabolism

e.g. using ATP to generate molecules such a glycogen and fatty acids via reduction

Question 38

anabolic processes are typically ________-ive

Answer 38

reductive

Question 39

A Bronsted-Lowry acid is a H+ ___________

A lewis acid is an electron pair ___________

Answer 39

H+ donor

electron pair acceptor

Question 40

K_{a =} ?/?

Answer 40

products / reactants

e.g. for a generic acid HA in water, the K_a 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

Question 41

higher K_a means ___\_stronger/weaker?___ acid

Answer 41

higher K_a 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 K_a than 2/3

Question 42

polyprotic acid

Answer 42

an acid that has more than 1 proton that can be donated (ie ionizable proton)

e.g. H2CO3

Question 43

a molecule is said to be amphoteric when ________

Answer 43

it can act as an acid or base

e.g. amino acid

Question 44

in water, since, [H+][OH-]=10^-14

we can derive the equation:

Answer 44

pH + pOH = 14

Question 45

in general, the “p” of something equals the -log of that something

Answer 45

true

Question 46

the higher the pKa, the _________ the acid

Answer 46

weaker

Question 47

buffer definition

Answer 47

a buffer is a solution that resists changing pH when a small amount of acid or base is added.

Question 48

buffering capacity is greatest when

Answer 48

the presence of a weak acid and its conjugate base are in equal concentrations

Question 49

Answer 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

Question 50

what characteristic of the peptide bond is responsible for a rigid primary structure? (no rotation about a single bond)

Answer 50

resonance, which creates a partial double bond of th peptide bond

Question 51

what does the secondary structure of proteins look like and what characterizes them?

Answer 51

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

Question 52

Tertiary structure is d/t ________interactions within a polypeptide

Answer 52

side chain

Question 53

Types of interactions that can make up tertiary structure

Answer 53

Non-Covalent

1. Polar/polar, nonpolar/nonpolar
2. electrostatic
3. acid/base

Covalent

1. disulfide bridges

Question 54

does a protein have to have all 4 levels of structure to be functional

Answer 54

no, but has up to tertiary

Question 55

Quarternary structure occurs d/t

Answer 55

side chain interactions between different polypeptides

Question 56

Definition of cofactor

Answer 56

A cofactor is a nonorganic molecule whose presence is necessary for the proper function of an enzyme.

Question 57

T/F: Entropy, enthalpy, and free energy are all thermodynamic quantities.

Answer 57

True

they cannot be considered when analyzing the catalytic effect of two different enzymes on a chemical reaction. (that’s kinetics)

Question 58

T/F: Denaturation of an enzyme will alter the kinetics of a reaction that it catalyzes.

Answer 58

True

Question 59

T/F: The kinetics of a reaction can be characterized by a rate-constant

Answer 59

True

Question 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.

Answer 60

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.

Question 61

The lock and key model states that _____

Answer 61

the active site of an enzyme matches the binding site of the substrate, which explains the specificity of enzymes for certain substrates

Question 62

A _____catalyzes the formation of a single bond between two substrates through the elimination of water.

Answer 62

ligase

Question 63

T/F: Catalysts make reactions fast by aligning reactants so that successful reactions are more likely!

Answer 63

True

Question 64

An enzyme not bound to its cofactor is called

Answer 64

Apoenzyme

Question 65

An enzyme bound to its cofactor is called

Answer 65

haloenzyme

Question 66

disulfide bonds are found in __\_intracellular/extracellular_____ polypeptides

Answer 66

extracellular, because inside the cell is a reducing environment

e.g. insulin, antibodies

Question 67

Phosphoglucomutase, which catalyses the formation of glucose-6-phosphate from glucose-1-phosphate, is best classified as which enzyme type?

Answer 67

isomerase, because glucose-6-phosphate is an isomer of glucose-1-phosphate.

Enzymes are classified according to the sort of reaction they catalyze.

Question 68

T/F: Enzymes can increase the rate of reactions that have a positive

Answer 68

FALSE

only reaction coupling can assist with this

Question 69

What are oxidoredutases?

Answer 69

“catalyze oxidation–reduction reactions that involve the transfer of electrons.” Movement of hydride is key to identifying REDOX reactions.

includes oxidases, reductases, dehydrogenases

Question 70

What are transferases?

Answer 70

“move a functional group from one molecule to another molecule.”

Kinase is an example of a transferase moving phosphate groups.

Question 71

What do hydrolases do?

Answer 71

“ catalyze cleavage with the addition of water.”

Most catabolic metabolism in the body is due to hydrolases.

Question 72

What are lyases?

Answer 72

Catalyze cleavage by means other than oxidation or hydrolysis reduction. The reverse reaction (synthesis) is often more important biologically.

Question 73

What are isomerases?

Answer 73

“ catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers.”

Question 74

What are ligases?

Answer 74

“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.

Question 75

Mnemonic for enzyme classifications?

Answer 75

LILHOT

Ligase, Isomerase, Lyase, Hydrolase, Oxidoreductase, Transferase.

Question 76

Why is the statement “An increase in the substrate concentration leads to proportional increases in the rate of the reaction” false?

Answer 76

As the reaction initially beings, this statement is true. Once the reaction hits Vmax, this statement stops being true.

Question 77

What are some characteristics of an enzyme?

Answer 77

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.)
5. Are pH- and temperature-sensitive, with optimal activity at specific pH ranges and temperatures
6. Do not affect the overall ΔG of the reaction
7. Are specific for a particular reaction or class of reactions”

Question 78

What are Kinases

Answer 78

enzymes that transfer a phosphate group to a molecule from a high energy carrier such as ATP (e.g. phosphofruktokinase)

this is a transferase

Question 79

What are polymerases?

Answer 79

catalyzes polymerization

e.g. addition of nucleotides to the leading strand of DNA by DNA polymerase III

Question 80

Phosphetase

Answer 80

removes a phosphate group from a molecule

Question 81

protease

Answer 81

hydrolyzes peptide bonds

e.g. trypsin, chymotrypsin, pepsin

Question 82

in ____________ a favorable reaction is used to drive an unfavorable one

Answer 82

reaction coupling

Question 83

cofactors are ___\_inorganic/organic___ molecules

Answer 83

inorganic

Question 84

What’s physical properties of the active site allow it to function?

Answer 84

they contain catalytic resides of AAs that are responsible for lowering the transition state

Question 85

What are the strategies/mechanisms by which enzymes do their job?

Answer 85

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

Question 86

Describe the induced fit model

Answer 86

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.

Question 87

If the enzyme-catalyzed reaction E + S ⇋ ES ⇋ E + P is proceeding at or near the V_max 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

Answer 87

S is abundant, [ES] is at its highest point

At V_max, 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 V_max there must be sufficient substrate for the enzyme to bind, so [S] must be high enough to sustain this saturated state.

Question 88

the magnitude of K_m depends on

Answer 88

environment and substrate concentration

Question 89

when [S] = K_m then how many active sites are bound?

Answer 89

exactly 1/2

which also means that [ES] = [E]_total / 2

it also means that V_not=V_max/2

Question 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?

Answer 90

There is low affinity

Question 91

when the K_-1 is >>> greater than k₂ the Michaelis constant Km describes

Answer 91

the likelihood of dissociation of the enzyme-substrate complex.

Question 92

a competitive inhibitor acts by:

Answer 92

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

Question 93

why is Vmax unaffected in the case of a competitive inhibitor?

Answer 93

because it is possible to add enough substrate to outcompete the inhibitor, which will yield the same Vmax as before

*this has to increase K_m, which is the substrate concentration required to get to 1/2 Vmax

Question 94

you have an enzyme-inhibitor complex. Adding more substrate allows you to reach Vmax eventually. what’s the type of inhibitor

Answer 94

competitive

Question 95

how does the graph for a competitive inhibitor differ from that of a non-competitive inhibitor?

Answer 95

Question 96

How does uncompetitive inhibition work?

Answer 96

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

Question 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.

Answer 97

non-competitive

Question 98

How does non-competitive inhibition work?

Answer 98

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 K_m 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 K_m)

Question 99

list the mechanisms of enzymatic control

Answer 99

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.

Question 100

What are the parts to a lineweaver burk plot and what’s its function?

Answer 100

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

Question 101

What does the lineweaver burk plot look like for a competitive inhibitor

Answer 101

Question 102

What does the lineweaver burk plot look like for a uncompetitive inhibitor?

Answer 102

Question 103

What does the lineweaver burk plot look like for a noncompetitive inhibitor?

Answer 103

Question 104

Cooperative enzymes must have:

1. exactly one active site
2. more than one

Answer 104

More than one

*this also means that they are likely to be multisubunit complexes

Question 105

T/F: increasing the temperature of an enzyme’s surroundings may or may not affect the likelihood of an enzyme binding its substrate

Answer 105

True.

UNLESS the temperature is increased to the point of denaturing

Question 106

K_m is can be used to measure binding affinity. because K_{m =} [E][S]/[ES], so as Km increases, binding affinity __________

Answer 106

decreases

Question 107

On a lineweaver-Burk plot, as Vmax decreases, the y intercept ________ (because y-intercept is 1/V_max)

Answer 107

increases

Question 108

DNA methylation occurs via addition of a methyl group to _______

Answer 108

cytosine, resulting in methyl-cytosine base-pairing with guanine.

Question 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.

Answer 109

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.

Question 110

T/F: increasing substrate concentration does not have an effect on K_m of an enzyme?

Answer 110

true

Question 112

What interactions maintain each type of protein structure?

Answer 112

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

Question 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

Answer 113

Energy storage

Question 114

T/F: reaction rate is independent of enzyme concentration.

Answer 114

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.

Question 115

Feedback inhibition involves the decrease in activity of an enzyme by _________

Answer 115

binding to a downstream product.

Question 116

an anti-substrate antibody binds to _______

Answer 116

the substrate

Question 117

does Vmax depend on substrate concentration?

Answer 117

NO

from the pic.. III. is wrong because its another way of saying competitive inhibition, which doesn’t change Vmax

Question 118

Answer 118

enzyme concentration always affects Vmax

Question 119

what is a zymogen

Answer 119

an inactive enzyme that requires a covalent modification

Question 120

define coenzyme

Answer 120

organic nonprotein molecules that bind with the protein molecule (apoenzyme) to form the active enzyme (holoenzyme).

Question 121

what’s the difference between a coenzyme and a cofactor?

Answer 121

a coenzyme is involved in helping catalysis

a cofactors participate in enzymatic activity

Question 122

what process serves as the principle energy source for cellular metabolism?

Answer 122

oxidation of carbohydrates (aka combustion)

Question 123

a glycosidic linkage is

Answer 123

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

Question 124

humans can’t digest which glycosidic linkage? what’s the exception

Answer 124

beta

with the exception of lactose.

Question 125

what’s the chemcial formula for a monosaccharide?

Answer 125

C_n H20_n

_{smallest functional monosaccharide is n=3}

Question 126

How do you determine the steriochemistry of monosaccharides?

Answer 126

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

Question 127

define epimer

Answer 127

a specific type of diateriomers that differ at only one carbon configuration

Question 128

How do you convert between a noncyclic monosacharide and its cyclic counterpart (present in equal amounts)

Answer 128

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

Question 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

Answer 129

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

Question 130

The epimers of glucose are

Answer 130

mannose and galactose

Question 131

sucrose is a mono or disacharide?

Answer 131

Sucrose is a disaccharide of fructose and glucose.

Question 132

define anomer

Answer 132

Anomers are epimers that are in their cyclic state.

Question 133

A furanose is a _____ membered ring featuring _______carbons and one oxygen.

Answer 133

five

4 carbons

Question 134

A pyranose is a _____ membered ring featuring _______carbons and one oxygen.

Answer 134

6

5 carbons

Question 135

The straight chain form of glucose differs from the straight chain form of fructose in which way?

Answer 135

Type of carbonyl functional group

Question 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 136

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).

Question 137

T/F:A glycosidic bond connects an anomeric carbon of one sugar to an alcohol oxygen of another sugar.

Answer 137

true

Question 138

T/F D-sugars have the same absolute configuration at the asymmetric center farthest from their carbonyl group as does D-glyceraldehyde.

Answer 138

True

Question 139

all D-Aldohexoses are diasteriomers of one another

Answer 139

true

Question 140

The chiral carbon furthest from the carbonyl group determines the absolute configuration of the sugar.

Answer 140

True: it tells you L or D, which is the absolute configuration

Question 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

Answer 141

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).

Question 142

Competitive Inhibition

binds at ?

effect on Vmax?

effect on Km?

Answer 142

Question 143

Uncompetitive Inhibitor:

binds at?

effect on Vmax?

effect on Km?

Answer 143

Question 144

Mixed inhibition

binds at?

effect on Vmax

effect on Km?

Answer 144

Question 145

What is the Gibbs free energy equation and what do each of the terms mean?

Answer 145

Question 146

T/F: delta G can tell you how fast a reaction will occur

Answer 146

false, only kinematics can tell you that. it only tells you whether a reaction is spontaneous

Question 147

all the macromolecules for the MCAT are _______________. Enzymes that make them are called ___________. Reactions that make them are called ____________ reactions

Answer 147

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)

Question 148

What’s a lipid made out of

Answer 148

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)

Question 149

what’s the difference between saturated and unaturated lipids/fats

Answer 149

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

Question 150

What are the forms of fatty acids in the body?

Answer 150

1. Triglyceride
2. Phospholipids
3. terpenes
4. cholesterol

Question 151

Describe a triglyceride?

Answer 151

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

Question 152

Describe a phospholipid aka phosphatides

Answer 152

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

Question 153

Describe a terpene

Answer 153

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

Question 154

describe cholesterol

Answer 154

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

Question 155

what would happen if you subjected your triglycerol to saponification

Answer 155

it would undergo base catalyzed hydrolysis into fatty acid salts plus glycerol

Question 156

who stores more energy content, carbohydrates or fats?

Answer 156

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.

Question 157

what are the structural determinants of membrane fluidity?

Answer 157

degree of saturation, tail length, amount of cholesterol

Question 158

what does an isporene unit look like?

Answer 158

has chemical formula C₅H₈

Question 159

what are sphingolipids

Answer 159

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

Question 160

what are waxes?

Answer 160

long chain fats esterified to long chain alcohols.

They are so hydrophobic that they form waterproof barriers in plants and earwax

Question 161

what defines the structure of a steroid?

Answer 161

having the same core tetracyclic ring system as cholesterol.

They are hydrophobic

Question 162

How do steroid hormones act on the body?

Answer 162

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.

*MCAT trick: don’t confuse steroid hormone with peptide hormones espeically in terms of receptor location

Question 163

What are the steroid hormones?

Answer 163

testosterone, estrogen, progesterone, aldosterone, cortisol

Question 164

what’s the main difference between steroid hormones and peptide hormones?

Answer 164

Peptide hormones exert their effects by binding to receotprs at the cell-surface.

steroid hormones diffuse into cells to find their receptors

Question 165

what are the peptide hormones?

Answer 165

insulin, glucagon, somatostatin, melatonin, erythropoetin, thrombopoetin, ANP, Thymosin

(not a complete list)

Question 166

what are the fat soluble vitamins and what structure do they have in common?

Answer 166

Vitamins A, E, D_3, K

mnemonic: get me the AED stat, K?!

all have ring structures

Question 167

Prostaglandins

Answer 167

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

Question 168

substrate analog

Answer 168

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

Question 169

what would be the most likely class of inhibitors that a substrate analog would belong too

Answer 169

competitive: because they need a property that allows them to take over/bind to the active site.

Question 170

Mechanisms of direct enzymatic regulation?

Answer 170

1. Removal of a phosphate with the use of a phosphatase
2. Peptide hydrolysis
3. Interaction of the enzyme with downstream products

Question 171

how are dietary fats broken down?

Answer 171

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.

Question 172

definition of denaturing

Answer 172

disruption of a proteins shape without breaking peptide bonds

e.g. misfolding

Question 173

what drives the folding of secondary structures such as alpha helixes into higher order tertiary structures?

Answer 173

interactions of R groups with each other and with the solvent

Question 174

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

Answer 174

Van der Waals and Covalent disulfide bonds

Question 175

quaternary structure

Answer 175

interactions between polypeptide subunits ie a multisubunit complex. peptide bonds do not contribute to quaternary structure, this belongs to primary

Question 176

carbohydrates can be broken down into CO₂ in a process called _______

Answer 176

oxidation

Question 177

What is pyrophsophate and how does its structure contribute to in being such a good energy source?

Answer 177

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

Question 178

what does a single unit of phosphoric acid vs phosphate look like?

Answer 178

phosphoric acid has 1 or more hydrogens still associated. At physiological pH, it becomes deprotonated, earning the name phosphate, or inorganic phosphate P_i (when unattached to organic matter)

Question 179

does starch have alpha or beta glycopsidic linkages?

Answer 179

alpha (basically same as glycogen)

Question 180

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

Answer 180

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).

Question 181

During the formation of a disaccharide, the __________group of one monosaccharide reacts with the _________ group of a second monosaccharide to form a glycosidic linkage.

Answer 181

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.