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MCAT > Biochem: Ch 8, 2, 3 > Flashcards

Biochem: Ch 8, 2, 3 Flashcards

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1
Q

fluid mosaic model

A

accounts for presence of lipids, proteins, and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells

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2
Q

carbohydrates in cell membrane

A

create glycoprotein coat

cell recognition

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3
Q

cell membrane dynamics

A

not static

  • lipids move freely in membrane thru diffusion and can assemble into lipid rafts
  • flippases maintain transport of lipids
  • proteins and carbohydrates move within membrane but are relatively slowed by large size
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4
Q

lipid rafts

A

collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules

serve roles in signaling

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5
Q

flippases

A

specific membrane proteins that maintain the bidirectional transport of lipids between the layers of the phospholipid bilayer in cells

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6
Q

list the following membrane components in order from post plentiful to least: carbs, lipids, proteins, nucleic acids

A

lipids > proteins > carbs > nucleic acids

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7
Q

triacylglycerols/triglycerides

A

storage lipids involved in human metabolic processes

contain 3 fatty acid chains esterified to glycerol molecule

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8
Q

tryglycerides and free fatty acids in membrane

A

act as phospholipid precursors

found in low levels in membrane

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9
Q

unsaturated fatty acids

A

have one ore more double bonds

impart fluidity to membrane

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10
Q

saturated fatty acids

A

main components of animal fats

decrease overal membrane fluidity

unhealthy

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11
Q

glycerolphospholipids

A

replace one fatty acid with phosphate group, which is often linked to toehr hydrophilic groups

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12
Q

cholesterol in cell membrane

A

present in large amounts

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13
Q

cholesterol

A

contributes to membrane fluidity and stability

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14
Q

waxes in cell membrane

A

present in small amounts

most prevalent in plants

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15
Q

waxes

A
  • extremely hydrophobic
  • waterproofing and defense
  • can provide stability and rigidity in nonpolar tail region of cell membrane
  • composed of long chain fatty acid and long chain alcohol –> high melting point
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16
Q

proteins located within cell membrane act as

A

transporters, cell adhesion molecules, and enzymes

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17
Q

transmembrane proteins

A

pass completely through lipid bilayer

can have one or more hydrophobic domains

most likely to function as receptors or channels

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18
Q

embedded proteins

A

associated with only the interior or exterior surface of cell membrane

most likely part of catalytic complex or involved in cellular communication

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19
Q

membrane associated (peripheral) proteins

A

act as recognition molecules or enzymes

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20
Q

extracellular ligands

A

bind to membrane receptors, which function as channels or enzymes in second messenger pathways

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21
Q

gap junctions

A

aka connexons

  • direct cell-cell communication
  • allow for rapid exchange of ions and other small molecules between adjacent cells
  • formed by alignment and interaction of pores composed of 6 molecules of connexin
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22
Q

tight junctions

A
  • prevent paracellular transport
    • prevent solutes from leaking into space between cells
  • do not provide intercellular transport
  • found in epithelial cells
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23
Q

desmosomes and hemidesmosomes

A

anchor layers of epithelial tissue together

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24
Q

phospholipids spontaneously assemble into

why?

A

micelles or liposomes

due to hydrophobic interactions

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25
Q

micelles

A

small monolayer vesciles

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26
Q

liposomes

A

bilayered vesicles

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27
Q

sphingolipids

A

contain hydrophilic region and two fatty acid derived hydrophobic tails

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28
Q

types of sphingolipids

A

ceramide, sphingomyelins, cerebrosides, gangliosides

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29
Q

desmosomes

A

bind adjacent cells by cnchoring to their cytoskeletons

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30
Q

hemidesmosomes

A

attach epithelial cells to underlying structures, esp basement membrane

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31
Q

three classes of membrane proteins

A

transmembrane proteins, embedded membrane proteins, membrane associated (peripheral) proteins

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32
Q

osmotic pressure

A
  • pressure applied to pure solvent to prevent osmosis
    • “sucking” pressure in which a solutions drawing water in, proportional to its conc
  • used to express the conc of the solution
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33
Q

passive transport

A

does not require energy bc molecule is moving down conc gradient or from an area with higher conc to area w lower conc

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34
Q

types of passive transport

A

simple diffusion, osmosis, facilitated diffusion

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35
Q

simple diffusion

A

passive transport

small, nonpolar molecules passively move from area of high conc to area of low conc until equilibrium is achieved

does not require transporter

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36
Q

osmosis

A

passive transport

diffusion of water across selectively permeable membrane

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37
Q

facilitated diffusion

A

passive transport

uses transport proteins to move impermeable solutes across cell membrane

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38
Q

active tranport

A

requires energy in form of ATP or an existing favorable ion gradient

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39
Q

types of active transport

A

primary, secondary

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40
Q

types of secondary active transport

A

symport, antiport

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41
Q

pinocytosis

A

ingestion of liquid into the cell in vescles formed from the cell membrane

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42
Q

phagocytosis

A

ingestion of larger, solid molecules

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43
Q

passive vs active transport

temperature

A

passive transport - can inc in rate as temp inc

active transport - may or may not be affected - depends on enthalpy

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44
Q

hypotonic solution

A

conc of solutes inside cell is higher than surrounding soln

causes cell to swell as water rushes in –> lysis

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45
Q

hypertonic solution

A

soln that is more conc outside the cell than inside

causes water to move out of cell

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46
Q

isotonic solution

A

solutions inside and outside cell are equimolar

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47
Q

osmotic pressure eq

A

II = iMRT

II = osmotic pressure

i = vant hoff factor = number of particles obtained from the molecule when ins oln

T = temp

M = molarity

R = ideal gas constant

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48
Q

carriers

A

only open to one side of cell membrane at any given point

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49
Q

occluded state

A

carrrier is not open to either side of membrane

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50
Q

primary active transport

A

uses ATP or another energy molecule to directly power the transport of molecules across membrane

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51
Q

secondary active transport

A

uses energy to transport particles across membrane by harnessing energy released by one particle going down its gradient to drive a different particle up its gradent

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52
Q

antiport

A

when both particles in secondary active transport move in opposite directions

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53
Q

symport

A

when both particles in secondary active transport move in same direction

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54
Q

endocytosis

A

ell membrane invaginates and engulfs material to bring it into cell

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55
Q

exocytosis

A

secretory vesicles fuse with membrane, releasing material from inside cell to extracellular environment

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56
Q

simple diffusion ex molecules transported

A

small, nonpolar

(O2, CO2)

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57
Q

osmosis ex molecules transported

A

h2o

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58
Q

facilitated diffusion ex molecules transported

A

polar molecules (glucose)

ions (Na+, Cl-)

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59
Q

active transport ex molecules transported

A

polar molecules or ions (Na+, Cl-, K+)

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60
Q

as osmotic pressure increases, water will tend to flow…

A

into the compartment to decrease solute concentration

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61
Q

osmotic pressure

water moves toward

A

compartment with highest osmotic pressure

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62
Q

primary thermodynamic factor responsible for passive transport

A

entropy

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63
Q

membrane potential is maintained by

A

sodium potassium pump and leak channels

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64
Q

electric potential created by one ion can be calculated using

A

nernst eq

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65
Q

resting potential of membrane at physiological temp can be calculated useing

A

goldman hodgkin katz voltage eq

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66
Q

how does mitochondrial membrane differ from cell membrane

A
  • outer mitochondrial membrane highly permeable to metabolic molecules and small proteins
  • inner membrane
    • citric acid cycle
    • enzymes
    • does not contain cholesterol
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67
Q

In the cell membrane, there are also the closely related Sphingolipids. Which of the following statements about Sphingolipids are true?

I. Sphingolipids lack Glycerol.
II. All Sphingolipids have a hydrophilic region and two fatty-acid like tails that form a hydrophobic region.
III. Some common Sphingolipids are Ceramide, Sphingomyelins, Gangliosides and Cerebrosides.

(A) II only
(B) I and II only
(C) I and III only
(D) I, II and III

A

(C) I and III only

Each of the following statements about Sphingolipids are true:

I. Sphingolipids lack Glycerol.
II. Sphingolipids have a hydrophilic region and can have either one or two fatty-acid like tails that form a hydrophobic region. Most have two, but not all do.
III. Some common Sphingolipids are Ceramide, Sphingomyelins, Gangliosides and Cerebrosides.

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68
Q

Describe whether or not each compound is able to pass through the Cell Membrane via Passive Diffusion:

(1) Gases
(2) Small, Polar Compounds
(3) Large, Non-polar Compounds
(4) Large, Polar Compounds
(5) Charged Compounds

A

(1) Gases - Yes, quickly.
(2) Small, Polar Compounds - Yes, slowly.
(3) Large, Non-polar Compounds - Yes, slowly.
(4) Large, Polar Compounds - No.
(5) Charged Compounds - No.

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69
Q

Which of the following are unable to pass through the Cell Membrane via Passive Diffusion?

I. Cholesterol
II. Na+
III. Glucose

(A) I Only
(B) I and II Only
(C) II and III Only
(D) I and III Only

A

(C) II and III Only

Cholesterol is a large, non-polar molecule, allowing it to pass through the Cell Membrane via Passive Diffusion at a slow rate.

Na+ is a charged compound, preventing it from utilizing Passive Diffusion.

Glucose is a large, polar compound, preventing it from utilizing Passive Diffusion.

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70
Q

Draw a Saturated Fatty Acid versus a Unsaturated Fatty Acid.

A
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71
Q

Compare Integral and Transmembrane Proteins.

A

Integral and Transmembrane proteins are the same exact thing! They both span the entire cell membrane from intracellular to extracellular.

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72
Q

Which of the following are roles that proteins play within a cell membrane?

I. Transport molecules
II. Transmit signals
III. Maintain the structural integrity of the cell membrane

(A) I Only
(B) II Only
(C) I and II Only
(D) I and III Only

A

(C) I and II Only

Proteins transport molecules across a cell membrane. They may also help transmit signals across a membrane.

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73
Q

CRB Define and draw a Glycoprotein.

A

Glycoprotiens are membrane-bound proteins that have an associated carbohydrate.
In this picture, the red is the membrane-bound protein.

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74
Q

Jack is studying a protein in his biochemistry class. He learns that this protein is located on the intracellular side of the cell membrane and converts one molecule into another molecule. This protein is known as a:

(A) lipidbound protein
(B) peripheral protein
(C) channel protein
(D) carrier protein

A

(B) peripheral protein

Peripheral proteins are on either the extracellular or intracellular side of the cell membrane but not both.

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75
Q

Your bladder needs to contain water without it leaking out into the rest of your body’s tissues. The cells in your bladder most likely utilize which cell junction to allow for this ability?

(A) Synapse Junctions
(B) Gap Junctions
(C) Desmosomes
(D) Tight Junctions

A

(D) Tight Junctions

Tight Junctions are waterproof seals. They are common in areas that contain large amounts of water such as the bladder, intestines, and the Kidney.

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76
Q

Which of the following statements about Gap Junctions are true?

I. Gap Junctions can also be called Connexons.
II. The pores of Gap Junctions are formed by pores in interacting Connexin molecules.
III. Molecules that flow between cells at Gap Junctions are said to follow a Paracellular Route.

(A) II only
(B) I and II only
(C) I and III only
(D) I, II and III

A

(B) I and II only

The Paracellular route is related to Tight Junctions. Each of the following statements are true about Gap Junctions:
I. Gap Junctions can also be called Connexons.
II. The pores of Gap Junctions are formed by pores in interacting Connexin molecules.

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77
Q

Which are able to move faster in the Plasma Membrane, Lipid Rafts or Phospholipids, and why?

(A) Phospholipids, because they are diffusing from high concentration to low concentration.
(B) Lipid Rafts, because they are diffusing from high concentration to low concentration.
(C) Phospholipids, because they are smaller than Lipid Rafts.
(D) Lipid Rafts, because they are only on the surface of the Plasma Membrane, whereas Phospholipids have tails entering the middle of the membrane.

A

(C) Phospholipids, because they are smaller than Lipid Rafts.

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78
Q

enzymes

A

biological catalysts that are unchanged by the reactions they catalyze and are reusable

lower the activation energy necessary for biological reactions

specific for a particular reaction or class of reactions

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79
Q

oxidoreductases

A

enzymes that catalyze redox rxns that involve the transfer of electrons

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80
Q

transferases

A

enzymes that move a functional group from one molecule to another molecule

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81
Q

hydrolases

A

enzymes that catalyze cleavage with the addition of water

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82
Q

lyases

A

enzymes that catalyze cleavage without the addition of water and without the transfer of electrons

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83
Q

isomerases

A

enzymes that catalyze the interconversion of isomers, including both constitutional isomers and steroisomers

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84
Q

exergonic reactions

A

release energy

ΔG < 0

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85
Q

what do enzymes NOT alter?

A

thermodynamics: free energy or enthalpy

equilibrium constant

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86
Q

what do enzymes alter?

A

rate at which equilibrium is reached

kinetics

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87
Q

reductant

A

electron donor in reactions catalyzed by oxidoreductases

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88
Q

oxidant

A

electron acceptor in reactions catalyzed by oxidoreductases

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89
Q

enzymes with dehydrogenase or reductase in their names are usually

A

oxidoreductases

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90
Q

enzymes with oxidase in their names usually

A

have oxygen as the final electron acceptor

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91
Q

kinases

A

type of transferase

catalyze the transfer of phosphate group, generally from ATP, to another molecule

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92
Q

major enzyme classifications

A

LIL HOT

  • Ligase
  • Isomerase
  • Lyase
  • Hydrolase
  • Oxidoreductase
  • Transferase
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93
Q

synthase

A

catalyze the synthesis of two molecules into a single molecule

(type of lyase)

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94
Q

ligases

A

enzymes that catalyze addition or synthesis reations, generally between large similar molecules

often require ATP

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95
Q

endergonic reaction

A

requires energy

ΔG > 0

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96
Q

mechanisms of enzyme activity

A

stabilize transition state –> provide favorable microenvironment

bond with substrate molecules

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97
Q

active site

A

site of catlysis

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98
Q

lock and key theory

A

enzyme and substrate are exactly complementary

no alteration of tertiary or quaternary structure is necessary

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99
Q

induced fit model

A

enzyme and substrate undergo conformational changes to interact fully

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100
Q

cofactors

A

metal cations or inorganic molecules that activate enzymes

often ingested as dietary materials

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101
Q

coenzymes

A

small organic molecules that active enzymes

often vitamins or derivatives of vitamins such as NAD+, FAD, and coenzyme A

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102
Q

substrate

A

molecule upon which an enzyme acts

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103
Q

apoenzymes

A

enzymes without their cofactors

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104
Q

holoenzymes

A

enzymes containing their cofactors

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105
Q

prosthetic groups

A

tightly bound cofactors or coenzymes that are necessary for enzyme function

106
Q

important coenzymes that must be replenished regularly and why

A

water soluble vitamins including B complex vitamins and ascorbic acid (vitamin C)

bc easily excreted

107
Q

major classes of vitamins

A

fat and water soluble

108
Q

enzymes experience ___ kinetics

A

saturation

109
Q

saturation kinetics

A

as substrate conc inc, reaction rate inc until a max value is reached

110
Q

cooperative enzymes display a sigmoidal curve on ___ plot because of

A

michaelis menton

the change in activity with substrate binding

111
Q

vmax

A

enzyme is working at maximum velocity

112
Q

only way to increase vmax

A

increasing enzyme conc

113
Q

michaelis-menten plot of enzyme kinetics

A
114
Q

michaelis menten rxn eq

A

ES complexes form at rate k1

ES dissociates at either rate k-1 or turn into E+P at rate kcat

[E] = enzyme

[S] = substrate

[P] = product

115
Q

michaelis menten eq

A
116
Q

Km

A

michaelis constant

  • substrate conc at which half of the enzyme’s active sites are full
  • can be a measure of the affinity of the enzyme for its substrate
  • intrinsic property of ES system
    • cannot be altered by changing conc
117
Q

low Km

A

high affinity for substrate

(low [S] required for 50% enzyme saturation)

118
Q

high Km

A

low affinity for the substrate

(high [S] required for 50% enzyme saturation)

119
Q

when [S] < Km

A

changes in substrate conc will greatly affect reaction rate

120
Q

when [S] > Km

A

reaction rate increases much more slowly as it approaches vmax

121
Q

kcat

A

turnover number

measures number of substrate molecules “turned over” or converted to product per enzyme molecule per second

122
Q

turnover number eq

A

vmax = [E]kcat

123
Q

catalytic efficiency

A

= kcat/Km

124
Q

high turnover results in

A

= large kcat

more efficient enzyme

125
Q

low turnover results in

A

= small kcat

less efficient enzyme

126
Q

lineweaver-burk plot

A

double reciprocal graph of Michaelis menten eq –> straight line

127
Q

lineweaver-burk plot used to

A

calculate values of Km and vmax

determine type of inhibition that an enzyme is experiencing

128
Q

lineweaver-burk plot

x intercept

A

-1/Km

129
Q

lineweaver-burk plot

y intercept

A

1/vmax

130
Q

subunits and enzymes exist in one of two states:

A

low affinity tense state (T)

high affinity relaxed state (R)

131
Q

hill’s coefficient

A

quantifies cooperativity

indicates the nature of binding by the molecule

132
Q

hill’s coefficient > 1

A

positively cooperative binding

133
Q

hill’s coefficient < 1

A

negatively cooperative binding

134
Q

hill’s coefficient = 1

A

no cooperative binding

135
Q

positively cooperative binding

A

after one ligand is bound, the affinity of the enzyme for further ligands increases

136
Q

negatively cooperative binding

A

after one ligand is bound, the affinity of the enzyme for further ligands decreases

137
Q

effects of increasing [S] on enzyme kinetics

A

depends on how much substrate there is to begin with

  • low [S]: inc in [S] -> inc in enzyme activty
  • high [S]: inc in [S] -> no effect on activity bc vmax has already been attained
138
Q

effects of increasing [E] on enzyme kinetics

A

increases vmax, regardless of starting conc of enzyme

139
Q

as Km inc, enzyme’s affinity for its substrate ___

A

dec

140
Q

effect on enzyme activity in vivo

A

temp and pH –> denaturing of enzyme and loss of activity due to loss of secondary, tertiary, or if present, quaternary structure

141
Q

effect on enzyme activity in vitro

A

salinity can impact action of enzymes

142
Q

ideal temp enzymes

A

37 deg C = 98 deg F = 310 K

143
Q

ideal pH for most enzymes

A

7.4

144
Q

feedback inhibition

A

aka negative feedback

regulatory mechanism whereby the catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway

145
Q

reversible inhibition

A

ability to replace the inhibitor with a compound of greater affinity or to remove it using mild lab equipment

146
Q

types of reversible inhibition

A

competitive, noncompetitive, mixed, uncompetitive

147
Q

competitive inhibition

A

inhibitor is similar to substrate and binds at active site

148
Q

how can competitive inhibition be overcome?

A

by adding more substrate

149
Q

competitive inhibition

vmax and Km

A

vmax = unchanged

Km = increases –> [S] has to be higher to reach vmax in the presence of inhibitor

150
Q

noncompetitive inhibition

A

inhibitor binds with equal affinity to the enzyme and the enzyme substrate complex

151
Q

noncompetitive inhibition

vmax and Km

A

vmax = dec –> less enzyme available to react

Km = unchanged –> any copies of enzyme that are still active maintain same affinity

152
Q

mixed inhibition

A

inhibitor binds with unequal affinity to enzyme and ES complex

153
Q

mixed inhibition

vmax and Km

A

vmax = dec

Km = depends on if inhibitor has a higher affinity for E or ES complex

  • if inhibitor preferentially binds to enzyme -> Km inc -> lowers the affinity
  • if inhibitor preferentially binds to ES -> Km dec -> increases affinity
154
Q

uncompetitive inhibition

A

inhibitor binds only with the ES complex and locks substrate into enzyme, preventing its release –> increases affinity between E and S

155
Q

uncompetitive inhibition

vmax and Km

A

vmax = dec

Km = dec

156
Q

feedforward regulation

A

enzymes regulated by intermediates that precede the enzyme in the pathway

157
Q

irreversible inhibition

A

active site is made unavailable for prolonged period of time or enzyme is permanently altered

158
Q

competitive inhibition

lineweaver burk plot

A
159
Q

noncompetitive inhibition

lineweaver burk plot

A
160
Q

uncompetitive inhibition

lineweaver burk plot

A
161
Q

allosteric enzyme

A

alternate between active and inactive form

162
Q

allosteric activator

A

binds to allosteric site and makes active site more available for binding to substrate

163
Q

allosteric inhibitor

A

binds to allosteric site and makes active site less available for binding to substrate

164
Q

enzymes can be covalently activated or deactivated by

A

phosphorylation or dephosphorylation

165
Q

enzymes and glycosylation

A

covalent attachment of sugar moities

can tag an enzyme for transport within cell or can modify protein activity and selectivity

166
Q

zymogens

A

precursors of active enzymes

167
Q

why are some enzymes released as zymogens

A

it is critical that certain enzymes (like digestive enzymes of pancreas) remain inactive until arriving at their target site

168
Q

structural proteins compose the

A

cytoskeleton, anchoring proteins, and much fo extracellular matrix

169
Q

most common structural proteins

A

collagen, elastin, keratin, actin, tubulin

170
Q

structural proteins

A

generally fibrous in nature

171
Q

motor proteins

A

have one ore more heads capable of force generation through a conformational change

have catalytic activity, acting as ATPases to power movement

172
Q

common applications of motor proteins

A

muscle contraction, vesicle movement within cells, cell motility

173
Q

most common motor proteins

A

myosin, kinesin, dynein

174
Q

binding proteins

A

bind a specific substrate, either to sequester it in the body or hold its concentration at steady state

175
Q

cell adhesion molecules (CAM)

A

allow cells to bind to other cells or surfaces

176
Q

CAM examples

A

cadherins, integrins, selectins

177
Q

cadherin

A

CAM

calcium dependent glycoproteins that hold similar cells together

178
Q

integrins

A

CAM

permit cells to adhere to proteins in extracellular matrix

some also have signaling capabilities

179
Q

selectins

A

CAM

allow cells to adhere to carbs on the surfaces of other cells

most commonly used in immune system

180
Q

antibodies (Ig)

role + structure

A

used by immune system to target specific antigen

contain constant region and variable region

two identical heavy chains and tow identical light changes

held together by disulfide linkages and noncovalent interactions

181
Q

motif

A

repetitive organization of secondary structural elements

182
Q

collagen

A

makes up most of extracellular matrix of connective tissue

strength and flexibility

183
Q

elastin

A

stretches and recoils, which restores original shape of tissue

184
Q

keratins

A

intermediate filament proteins found in epithelial cells

found in hair and nails

185
Q

actin

A

protein that makes up mcirofilaments and thin filaments in myofibrils

have a positive and negative side that allows motor proteins to travel along this filament

186
Q

tubulin

A

makes up microtubules

negative and positive end

187
Q

myosin

A

primary motor protein that interacts with actin

can be involved in cellular transport

188
Q

kinesins and dyneins

A

motor proteins assoiated with microtubules

189
Q

ungated channels

A

always open

190
Q

voltage gated channels

A

open within a range of membrane potentials

191
Q

ligand gated channels

A

open in presence of specific binding substance, usually hormone or neurotransmitter

192
Q

enzyme linked receptors

A

participate in cell signaling thorugh extracellular ligand binding and imitation of second messenger cascades

193
Q

g protein coupled receptors

A

have membrane bound protein associated with a trimeric G protein

initiate second messenger system

194
Q

GPCR steps

A
  1. ligand binding engages G protein
  2. GDP replaced with GTP
    1. alpha subunit dissociates from beta and gamma subunits
  3. activated alpha subunit alters activity of adenylate cyclase or phospholipase C
  4. GTP is phosphorylated to GDP
    1. alpha subunit rebinds to beta and gamma subunits
195
Q

membrane spanning domain

A

anchors receptor in cell membrane

196
Q

ligand binding domain

A

stimulated by appropriate ligand and induces a conformational change that activates catalytic domain

197
Q

classic example of second messenger cascade

A

receptor tyrosine kinases (RTKs) - phosphorylate other enzymes

198
Q

electrophoresis

A

uses gel matrix to observe migration of proteins in response to electric field

subjects compounds to electric field, which moves them according to their net charge and size

199
Q

native PAGE

A

gel electrophoresis

maintains protein’s shape, but results are difficult to compare because mass to charge ratio differs for each protein

200
Q

SDS PAGE

A

gel electrophoresis

separates proteins on the basis of relative molecular mass alone

denatures the proteins and masks the active charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel

201
Q

isoelectric focusing

A

gel electrophoresis

separates proteins by their isoelectric point

protein migrates toward an electrode until it reaches a region of the gel where pH = pI of the protein –> protein takes on neutral charge and will stop moving

202
Q

chromatography

A

separates protein mixtures on bases of their affinity for a stationary or mobile phase

203
Q

column chromatography

A

uses beads of polar compound with nonpolar solvent

204
Q

ion exchange chromatography

A

uses charged column and variably saline eluent

205
Q

size exclusion chromatography

A

relies on porous beads

larger molecules elute first

206
Q

affinity chromatography

A

uses bound receptor or ligand and an eluent with free ligand or receptor for the protein of interest

207
Q

homogenization

A

crushing, grinding, or blending the tissue of interest into evenly mixed solution

208
Q

centrifugation

A

isolates proteins from much smaller molecules before other isolation techniques must be employed

209
Q

electrophoresis

negatively charged compounds will migrate toward

A

positively charged anode

(A+ Anode has acidic gel and + charge)

210
Q

electrophoresis

positively charged compounds will migrate toward

A

negatively charged cathode

211
Q

polyacrylamide gel

A

standard medium for protein electrophroesis

allows smaller particles to pass through easily while retaining large particles

212
Q

polyacrylamide gel

molecules will move faster if they are

A

small, highly charged, or placed in large electric field

213
Q

polyacrylamide gel

molecules will move slower if they are

A

bigger, more convoluted, electrically neutral, or placed in small electric field

214
Q

PAGE is most useful to

A

compare the molecular size or charge of proteins known to be similar in size from other analytic mehods

215
Q

isoelectric point (pI)

A

pH at which the protein is electrically neutral

216
Q

partioning

A

separation of components within stationary phase

217
Q

what are two potential drawbacks of affinity chromatography?

A
  1. protein of interest may not elute from column bc its affinity is too high
  2. may be permanently bound to free receptor in eluent
218
Q

x ray crystallography

A

determines protein structure after protein is isolated

measures electron density on high res scale

219
Q

edman degradation

A

sequential degradation for amino acid sequencing

uses cleavage to sequence proteins

220
Q

how are activity levels for enzymatic samples determined?

A

following the process of a known reaction, often accompanied by a color change

221
Q

protein conc can be determined

A

colorimetrically, either by UV spectroscopy or through color change reaction

222
Q

assays that test for protein

A

BCA assay, Lowry reagent assay, Bradford protein assay

223
Q

bradford protein assay

A

uses color change from brown-green to blue

most common assay

224
Q

protein structure can be determined through

A

X-ray crystallography and NMR spectroscopry

225
Q

CRB Compare Enzymes and Catalysts.

A

Catalysts are any material that are not used up in a reaction, but can speed up the process of a reaction.

Enzymes are Biological Catalysts made of proteins. Also note that there are Ribozymes (RNA that can have catalytic functions similar to protein enzymes).

226
Q

Describe the relationship between antibodies and antigens

A

Antigens are the ligands of antibodies. If an antigen is not recognized as belonging to the host, the antibody can recognize and flag this protein for elimination or degradation.

227
Q

Which motor protein(s) is/are specifically responsible for intracellular transport?

I. Myosin
II. Kinesin
III. Dynein

(A) I Only
(B) III Only
(C) I and II Only
(D) II and III Only

A

(D) II and III Only

Kinesin and dynein are motor proteins that are responsible for intracellular transport.

228
Q

At which point of a reaction do the enzyme and substrate bind at their maximum strength?

(A) Just before the Transition State
(B) During the Transition State
(C) Just after the Transition State
(D) At the end of a reaction

A

(B) During the Transition State

The enzyme is most tightly bound to its substrate during the transition state (induced fit stage).

229
Q

What occurs at the active sites vs. allosteric sites of an enzyme?

A

The active site is where the reaction takes place, while the allosteric site is where regulation takes place.

230
Q

Describe the mechanism of action for a ligase enzyme.

A

Ligase enzymes catalyze reactions between molecule A and molecule B to form a complex molecule AB.

231
Q

Describe the mechanism of action for an oxidoreductase enzyme? Oxidase enzyme? Reductase enzyme?

A

Oxidoreductase enzymes can catalyze both oxidation and reduction reactions.

Oxidase enzymes catalyze reactions that take electrons away from a molecule.

Reductase enzymes catalyze reactions that give electrons to a molecule.

232
Q

Fill in the blanks: In an Oxidoreductase enzyme’s reactions, the electron donor is called the _____________, and the electron acceptor is called the ____________. This is more closely related to the ____________ definition of Acids and Bases.

(A) Reductant, Oxidant, Bronsted-Lowry
(B) Reductant, Oxidant, Lewis
(C) Oxidant, Reductant, Bronsted-Lowry
(D) Oxidant, Reductant, Lewis

A

(B) Reductant, Oxidant, Lewis

In an Oxidoreductase enzyme’s reactions, the electron donor is called the Reductant, and the electron acceptor is called the Oxidant. This is more closely related to the Lewis definition of Acids and Bases.

233
Q

During DNA replication, two strands of DNA are joined together. What kind of enzyme would be involved in this reaction?

(A) Hydrolase
(B) Ligase
(C) Lyase
(D) Transferase

A

(B) Ligase

A ligase enzyme (DNA ligase) is involved in DNA replication because two separate DNA strands (molecules) are being joined to form a single strand.

234
Q

CRB Compare Lyases and Ligases.

A

Both Lyases and Ligases can catalyze synthesis reactions without Oxidation-Reduction occurring.
Lyases can also catalyze the splitting of these bonds without water or Oxidation-Reduction occurring, and typically work with small molecules. This 2nd reaction is what lyases are typically known for.
Ligases typically work with larger molecules and require ATP.

235
Q

What is the difference between vitamins and minerals?

A

Vitamins are carbon-based (organic) co-enzymes, whereas minerals are inorganic or metallic co-factors. Minerals may also help structurally, such as calcium, which is an important component of bone and teeth.

236
Q

How can we increase the rate of a reaction assuming the rate constant (k) is constant?

I. Increase Substrate Concentration
II. Increase Enzyme Concentration
III. Increase Mixed Inhibitor Concentration

(A) I Only
(B) I and II Only
(C) II and III Only
(D) I, II, and III

A

(B) I and II Only

We can increase the rate of reaction by increasing the substrate or enzyme concentration.

Adding any type of inhibitor will not increase the rate of a reaction.

237
Q

What is the steady-state assumption when talking about enzyme kinetics?

(A) [ES] is constant
(B) [S] is constant
(C) [P] is constant
(D) [I] is constant

A

(A) [ES] is constant

The steady state assumption means that the concentration of the enzyme-substrate complex (ES) is constant, which means that the formation of ES is equal to the dissociation of ES.

238
Q

The catalytic efficiency for a certain reaction increases. What happens to the reaction rate?

(A) It would increase
(B) It would remain the same
(C) It would decrease
(D) It would stop

A

(A) It would increase

Catalytic efficiency is basically an enzyme’s ability to catalyze reactions. If it increases so too will the rate of the reaction.

239
Q

What is the equation for the enzyme turnover number (Kcat)?

A

Kcat = Vmax/ [E]T

Vmax is the maximum velocity of the enzyme

[E]T is the concentration of the enzyme.

unit: 1/sec

240
Q

What does the enzyme turnover number (Kcat) really mean?

A

The enzyme turnover number (Kcat) basically tells us how many substrates a single enzyme can turn into product in one second at its maximum speed.

241
Q

Draw a Lineweaver-Burke plot. What is the equation for the x- and y- intercept? What about the slope?

A
242
Q

Which type of inhibitor will decrease Vmax but does not apparently alter the value of Km?

(A) Competitive
(B) Uncompetitive
(C) Noncompetitive
(D) Mixed

A

(C) Noncompetitive

A noncompetitive Inhibitor will decrease Vmax and not alter the value Km.

A noncompetitive inhibitor decreases Vmax because it binds to enzyme and the enzyme-substrate complex, thus creating less available enzymes to react.

The inhibitor binds ES, shifting the reaction (E + S –> ES) to the right. The inhibitor also binds to E, shifting the reaction to the left. Furthermore, the inhibitor binds to ES and E with the same affinity; this means these shifts cancel each other out, resulting in no change to affinity (Km).

243
Q

What type of inhibitor does not change the apparent Km value?

(A) Competitive
(B) Uncompetitive
(C) Noncompetitive
(D) Mixed

A

(C) Noncompetitive

A noncompetitive inhibitor does not change the apparent Km value because the inhibitor binds equally well to the enzyme and enzyme-substrate complex.

244
Q

What type of inhibitor does not change the Vmax value?

(A) Competitive
(B) Uncompetitive
(C) Noncompetitive
(D) Mixed

A

(A) Competitive

Competitive inhibitor does not change the Vmax value because if enough substrates are added, it will outcompete the inhibitor and be able to run the reaction at maximum velocity.

245
Q

On a Michaelis-Menten plot please draw what the curves would look like for enzymes with non-cooperative binding, positive-cooperative binding, and negative-cooperative binding.

A

An enzyme with non-cooperative binding will have a hyperbolic shaped curve.

An enzyme with positive-cooperative binding will have a sigmoidal “S” shaped curve.

An enzyme with negative-cooperative binding will have an altered hyperbolic shape with a steeper initial curve than non-cooperative binding.

246
Q

Draw the percent saturation curves of Hemoglobin and Myoglobin. How do they differ?

A

Hemoglobin has a sigmoidal “S” shaped curve because it exhibits positive-cooperative binding. Myoglobin has a hyperbolic curve since it exhibits non-cooperative binding.

247
Q

CRB Compare how drastically increasing and decreasing pH can differently cause Denaturation.

A

Increasing pH will cause deprotonation of key residues in the active site and affect hydrogen bonding of the secondary structure. Decreasing pH could protonate key residues in the active site, also affecting the hydrogen bonding of the secondary structure, and could also protonate the Cystines, breaking all disulfide bonds.

248
Q

How could dramatically increasing the Salinity of an solution with enzymes denature the enzyme?

(A) It could disrupt the Primary Structure by breaking only covalent bonds.
(B) It could disrupt Secondary Structure by disrupting only Hydrogen Bonds.
(C) It could disrupt Tertiary and Quaternary Structure by disrupting only Ionic Bonds.
(D) It could disrupt Secondary, Tertiary and Quaternary Structure by disrupting both Hydrogen and Ionic Bonds.

A

(D) Increased Salinity could disrupt Secondary, Tertiary and Quaternary Structure by disrupting both Hydrogen and Ionic Bonds.

249
Q

Compare the two types of enzyme regulators – allosteric activators vs. inhibitors. How does each affect Km and Vmax?

A

Allosteric activators increase enzyme activity. They increase Vmax and decrease Km.

Allosteric inhibitors decrease enzyme activity. They decrease Vmax and increase Km.

250
Q

A single reaction in a pathway would be a great control point for regulation if it has a very:

(A) positive ΔG.
(B) negative ΔG.
(C) positive ΔS.
(D) negative ΔS.

A

(B) negative ΔG.

A reaction with a negative ΔG would be a great “committing” step for a pathway because that reaction is unlikely to be reversed. That reaction’s products would then be committed to moving forward in the pathway. Phosphofructokinase’s reaction has a very negative ΔG; thus, it is a great control point for glycolysis.

251
Q

Match each of the following types of Gel Electrophoresis with their descriptions.

I. Polyacrylamide Gel.
II. Native PAGE
III. SDS-PAGE

(A) Can only give mass-to-charge ratios, so could have decreased separation of proteins with different masses or charges. This does NOT denature the protein.
(B) The typical medium used for protein electrophoresis.
(C) Uses a Detergent to break all noncovalent interactions, including affecting the charges of proteins. They are only separated based on size.

A

Note that PAGE stands for Polyacrylamide Gel Electrophoresis

I. Polyacrylamide Gel - (B) The typical medium used for protein electrophoresis.

II. Native PAGE - (A) Can only give mass-to-charge ratios, so could have decreased separation of proteins with different masses or charges. This does NOT denature the protein.

III. SDS-PAGE - (C) Uses a Detergent to break all noncovalent interactions, including affecting the charges of proteins. They are only separated based on size.

252
Q

Which of the following descriptions of Isoelectric Focusing are true?

I. The gel that the samples are separated in has a pH gradient, ranging from acidic to basic.
II. The protein will settle at the pH where the protein’s R-groups are fully deprotonated.
III. As proteins move towards the Cathode, the pH increases.

(A) I only
(B) I and III only
(C) II and III only
(D) I, II and III

A

(B) I and III only

Each of the following statements are true about Isoelectric Focusing:

I. The gel that the samples are separated in has a pH gradient, ranging from acidic to basic.
II. The protein will settle at the pH equal to the protein’s pI.
III. As proteins move towards the Cathode, the pH increases.

253
Q

CRB True or false? In isoelectric focusing, the proteins are loaded near the Anode, where there is a low pH and the proteins will be protonated and positively charged.

A

True. In isoelectric focusing, the proteins are loaded near the Anode, where there is a low pH and the proteins will be protonated and positively charged.

254
Q

Which of the following are examples of Membrane Receptors?

I. Ligand-gated Ion Channels
II. G-protein Coupled Receptors
III. Enzyme Linked Receptors

(A) I and II Only
(B) II and III Only
(C) I and III Only
(D) I, II, and III

A

(D) I, II, and III

The following are examples of Membrane Receptors:

I. Ligand-gated Ion Channels
II. G-protein Coupled Receptors
III. Enzyme Linked Receptors

255
Q

The GPCR mechanism is extremely important to know. Please draw out this mechanism, including the α, β, and γ subunits of the G Protein.

A
256
Q

Epinephrine is a classic example of a molecule that binds to a GPCR. In this case, the activated α-subunit binds to Adenylate Cyclase. What does Adenylate Cyclase then do?

A

Adenylate Cyclase converts ATP into cAMP (Cyclic AMP), which will then activate and alter other proteins within the cell, ultimately resulting in increased heart rate, dilated blood vessels, glycogenolysis, etc.

257
Q

Receptor Tyrosine Kinases (RTKs) are classic examples of Enzyme linked receptors. After a ligand binds to the Ligand Binding Domain, what cascade of events occurs in order to activate intracellular proteins?

A

Upon activation, neighboring RTKs will move close together and form cross-linked dimers. Next the Tyrosine amino acids in the Enzymatic Domain will phosphorylate each other. Now, these Phosphorylated Tyrosine amino acids can bind to intracellular proteins and activate them.

258
Q

CRB Recall the equation for Gibbs Free Energy. What must be increasing to make Passive Transport have a negative ΔG?

A

It is illogical to think that this Passive Transport will significantly increase temperature, so this Passive Transport must increase Entropy.

259
Q

CRB What is the significance of the Van’t Hoff Factor in that Osmotic Pressure equation?

A

The Van’t Hoff Factor is the number of particles that are in solution for each molecule of the substance that dissolved. This is how you account for the number of molecules in solution being different when ionic solutions dissolve into multiple particles!

260
Q

CRB Mitochondria also have two membranes. Compare the permeabilities of each membrane.

A

The Outer Mitochondrial membrane has many large pores, allowing ions and small proteins to move freely, including electron carriers.
The Inner Mitochondrial Membrane is much less permeable, requiring the integral proteins that are part of the Electron Transport Chain and ATP Synthase for the passage of ions to occur.

MCAT (26 decks)

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