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Bio Chem 501 > Unit 1 > Flashcards

Unit 1 Flashcards

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1
Q

H-H Equation

A

pH = pKa + log (A- / HA)

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2
Q

Kw Equation

A

10^-14 = (H+) x (OH-)

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3
Q

pKa > pH

A

Protonated

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4
Q

Main Cell Parts (4)

A

Cytoplasm
Plasma membrane
DNA
Ribosomes

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5
Q

Free Energy Equation

A

ΔG = ΔH - TΔS

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6
Q

Rate Law

A

Rate (Product) = k [Reactants]

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7
Q

What is Keq

A

Keq = (kforward / kreverse)

How far a reaction proceeds in a net direction until equilibrium is reached

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8
Q

RNA World Hypothesis

A

Life may have started with a self-replicating RNA

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9
Q

Why is RNA possibly the start of life

A

RNA is a carrier of genetic info

RNA is a catalyst

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10
Q

Phosphate Buffer

A

Ionization is important

Buffer important for maintaining pH in cells

Decent butter (5.86 to 7.86)

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11
Q

Bicarbonate

A

Buffer important for maintaining pH in blood

Equilibrium with CO2 (g)

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12
Q

Isoelectric Point

A

pH where net charge = 0

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13
Q

How does a peptide bond form

A

Condensation Rxn

Middle amino acids lose their amino and carboxyl ends

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14
Q

Post Translational modification

A

After a protein is made in the cell, it can be chemically modified by enzymes

Enzymes that modify proteins recognize specific target peptide sequences

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15
Q

What proteins are detected by UV

A

Tryptophan
Tyrosine (inefficient)

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16
Q

Ion Exchange Chromatography

A

Column is the stationary phase (opposite charge than proteins)

Positive proteins stick to negative beads

Proteins move through column at a speed dependent on net charge

Most attracted = last and least attracted = first

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17
Q

Remove protein from ion exchange chromatography

A

Change the salt conditions

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18
Q

Size Exclusion Chromatography

A

Porous column = molecular sieve

Smaller molecules get stuck in pores

Largest molecules come off first, smallest molecules are last

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19
Q

Affinity Chromatography

A

Protein interacts with ligand and is captured

Unwanted proteins come off first

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20
Q

Remove protein from affinity chromatography

A

Use excess free ligand

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21
Q

Specific activity

A

Specific activity = purity of protein

Specific activity = (activity / total protein)

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22
Q

Electrophoresis

A

Separation on the basis of charge via eclectic field

Separation based on size when the protein is denatured by a detergent (SDS Page)

Negative proteins move to positve end

Method to separate proteins based on their charge and size

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23
Q

SDS Page

A

Codes all proteins with a negative charge

Unfolds proteins for constant shape

Detergent

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24
Q

Isoelectric Focusing

A

Protein sample applied to an end of a gel strip with pH gradient

pH goes from high to low (basic to acidic)

Method to separate proteins based on their isoelectric point

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25
Q

Mass Spectrometry

A

Get molecules to fly in gas phase (electrospray ionization)

Separate ions by mass in a vacuum

Method to determine the mass and sequence of proteins

Lighter ones go further
Protein gains + charge

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26
Q

Primary Structure

A

Sequence of amino acids

Peptide bond is planar due to partial double bond (C - N)

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27
Q

Secondary Structure

A

Local 3D configuration

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28
Q

Tertiary Structure

A

Multiple secondary structures together

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29
Q

Quaternary Structure

A

Assembled subunits (tertiary structures)

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30
Q

Alpha Helix

A

3 amino acids per turn

Right handed

Side chains protrude out

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31
Q

of H-bonds in a helix

A

Number of amino acids - 4

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32
Q

of Turns in a Helix

A

(# of amino acids) / 4

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33
Q

Length of a Helix

A

(# of turns) x (A length)

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34
Q

Beta Sheet

A

Hydrogen bonds formed between strands

Sheets have a twist (not flat)

Side chains on alternate sides of the sheet (pleated)

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35
Q

Parallel Beta Sheet

A

Strands run in the same direction

Less stable due to H-bonds at an angle

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36
Q

Antiparallel Beta sheet

A

Strands run in opposite directions

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37
Q

Tertiary structure motif

A

Tertiary structures made from arrangements of secondary structures

Smaller tertiary units make bigger tertiary structures

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38
Q

Source of protein stability

A

Hydrophobic effect

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39
Q

Why do proteins have a size limit

A

More efficient to build large structures from lots of small ones

Error rate of protein synthesis is 1 mistake per 10,000 amino acids

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40
Q

Fibrous Proteins

A

Highly extended
Exhibit repeating structure

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41
Q

Fibrous Proteins Ex

A

Keratin, collagen

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42
Q

Globular Proteins

A

Compact
Globe shaped

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43
Q

Heme Binding Iron

A

Porphyrin ring provides 4 N ligands to iron (helps stabilize Fe2+)

Protein fold stabilizes Fe2+ (binds O2)

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44
Q

R to T Change

A

Oxygen binding moves the histidine → pulls on the helix → changes to R state

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45
Q

Oxygen + R State

A

Oxygen binds more strongly to R state

Stabilizes R state

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46
Q

Kd

A

concentration when 50% of the ligand is bound

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47
Q

Myoglobin

A

Not suitable as an oxygen transporter

Binds oxygen too tightly

Monomer (no 4° structure)

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48
Q

Hemoglobin

A

Tetramer

Blood transporter

4 binding sites for oxygen

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49
Q

Cooperativity

A

Binding of the first molecule allows subsequent molecules to bind more tightly

Subunits coordinate with each other

50
Q

CO2 + Hemoglobin

A

CO2 binds to amino end of terminal amino acid

51
Q

H+ and Hemoglobin

A

H+ binds to side chains

52
Q

Bohr Effect

A

Binding affinity for oxygen decreases at lower pH

Low pH stabilizes the T state

Favors uptake of protons and release of O2 in the tissues

53
Q

BPG Binding

A

BPG binds in the cavity between the subunits in the T state

54
Q

BPG + Affinity

A

BPG lowers binding affinity of hemoglobin for oxygen

Stabilizes the T state

55
Q

Properties of Enzymes

A

Usually protein

Incredible catalysts

Highly specific

Provide control over metabolic processes

3D structure is important for activity

Essential for Life

56
Q

Enzymes Complementary to

A

The TS (Transition State)

57
Q

Acid Base Catalysis

A

Enzyme provides additional functional groups that help in catalysis once the substrate is bound

General acids and bases are contributors

58
Q

Covalent Catalysis

A

Formation of covalent bond between enzyme and substrate

Bond must break in order to release product/regenrate enzyme

59
Q

Metal Ion Catalysis

A

Positive metal ions stablize negative transition states

60
Q

Fetal Hemoglobin

A

Lower affinity for BPG
Higher affinity for O2

Mother must have more R State

61
Q

Catalytic efficiency

A

Kcat/Km

62
Q

Enzymes controlled by

A

Equilibrium constant

63
Q

Chymotrypsin: Ser

A

Covalent catalysis

64
Q

Chymotrypsin: His

A

General acid-base catalysis

65
Q

Chymotrypsin: Oxyanion Hole

A

Lowers Ea by stabilizing oxyanion in TS

66
Q

Chymotrypsin: Hydrophobic pocket

A

Substate binding and specificity

67
Q

Regulatory enzymes

A

Must exhibit decreased or increased activity in response to signals

68
Q

Allosteric Enzymes

A

Change shape
Non MM
Catalytic and regulatory subunits

69
Q

Regulatory subunit

A

Binds modulator –> conformation change –> enzyme more active

70
Q

Catalytic subunit

A

Binds the substrate

71
Q

Feedback inhibition

A

Product shuts down its own synthesis by negatively regulating an enzyme in the synthesis pathway

72
Q

Covalently Modified enzymes

A

Regulatory compounds are covalently attached in a reversible matter

73
Q

Zymogens

A

Made as inactive precursors that need to be cleaved to become active

74
Q

Reversible inhibition

A

Small molecules that bind in or close to active site

75
Q

Competitive Inhibition

A

Inhibitor binds to free enzyme

Inhibitor competes for active site

Affects Km

76
Q

Uncompetitive Inhibition

A

Inhibitor binds to ES complex

Km and Vmax affected equally

77
Q

Mixed Inhibition

A

Mixture of competitive and noncompetitive

Bind to active site or ES complex

Affects all parameters unequally

78
Q

Inhibition Y Int

A

1/Vmax

79
Q

Inhibition X Int

A

-1/Km

80
Q

Irreversible inhibition

A

Covalently attach to enzyme

Covalent modification of the active site

81
Q

Fatty acids

A

Carboxyl head (polar)

Aliphatic tail (hydrocarbon chain)

Named based on # of carbons

82
Q

Saturated fatty acids

A

Solid at room temp

Higher melting point than unsaturated

83
Q

Unsaturated fatty acids

A

Kink from double bond interferes with packing

Lower MP

84
Q

Hydrogenation

A

Add H across double bond (increase MP)

85
Q

Chymotrypsin Step 1

A

Substrate binds to hydrophobic pocket

86
Q

Chymotrypsin Step 2

A

Histidine acts as a general BASE to activate a serine OH group

87
Q

Chymotrypsin Step 3

A

A serine alkoxide ion attacks a carbonyl carbon of the substrate, forming a
covalent acyl bond between enzyme and substrate.

88
Q

Chymotrypsin Step 4

A

A tetrahedral transition state involving an oxyanion is stabilized by the
oxyanion hole

89
Q

Chymotrypsin Step 5

A

Histidine acts as a general acid to protonate an amide nitrogen.

The peptide bond is broken and the first product dissociates.

90
Q

Chymotrypsin Step 6

A

Water enters the active site

91
Q

Chymotrypsin Step 7

A

Histidine acts a general base to convert water into a hydroxide ion

92
Q

Chymotrypsin Step 8

A

A hydroxide ion attacks the acyl bond between substrate and enzyme

93
Q

Chymotrypsin Step 9

A

A tetrahedral transition state involving an oxyanion is stabilized by the oxyanion hole

94
Q

Chymotrypsin Step 10

A

Histidine acts as a general acid to protonate the serine oxygen group, breaking the acyl bond between enzyme and substrate.

The second product
dissociates.

95
Q

Why triacylglycerols are good for the energy storage

A

Highly reduced

Provide 2X energy as cards

Dehydrated (less space than carbs)

96
Q

Disadvantage of triacylglycerols

A

Metabolized more slowly than carbs

97
Q

Glycerophospholipids

A

Phospho group - polar head group

Glycerol 3 phosphate = backbone

2 x fatty acids

98
Q

Sphingolipids

A

Backbone = sphingosine

1 x fatty acid

Amide linkage

Can have chains of sugars

99
Q

How lipids can be converted into signaling molecules

A

Prostaglandin = derivative of glycerophospholipids

Enzymes break bonds and release acid

Acid is modified by enzymes

100
Q

Sterols

A

Alkyl tail and polar head

Steroids derived from cholesterol

101
Q

Hormones

A

Derived from steroid nucleus of cholesterol

No tail

More hydrophilic

102
Q

Membrane compartments

A

ER

Nucleus

Mitochondria

Granules

103
Q

Liposomes

A

Bilayers wrap around to form continuous, spherical particles

104
Q

Dynamics

A

Uncatalyzed transbilayer (flip flop) is very slow

Uncatalyzed lateral diffusion is very fast

105
Q

Fluidity in membranes

A

High temp → decrease unsaturated fatty acids

Low temp → increase unsaturated fatty acids

106
Q

Hydrogen Bonding

A

Longer and weaker bond than covalent bonds, prefer 180° angle and 1.8 A distance

107
Q

Myoglobin

A

Oxygen storage protein

108
Q

Reversible Inhibition

A

Inhibition of enzyme activity by small molecules

109
Q

Irreversible Inhibition

A

Covalent modification of enzymes to permanently inhibit their activity

110
Q

Peripheral Membrane Proteins

A

Proteins that are loosely associated with the membrane

111
Q

Integral membrane proteins

A

Tightly associated with membrane
Require detergent to remove

112
Q

Beta Barrel

A

Hydrophobic part faces bilayer
Hydrophilic part lines pore
Facilitated diffusion

113
Q

Passive transport

A

Diffusion along a gradient
No energy required

114
Q

Passive transport types

A

Simple
Facilitated

115
Q

Simple diffusion

A

Diffusion along a membrane
No protein

116
Q

Facilitated diffusion

A

Requires protein carrier

Channels (pores or 1 gate)
Passive transporters (2 gates)

117
Q

Active transport

A

Against the gradient
Requires energy

118
Q

Active transport types

A

Primary
Secondary

119
Q

Primary transport

A

Requires atp
Ion pumps

120
Q

Secondary transport

A

Requires existing gradient
Gradient drives cotransport

Bio Chem 501 (4 decks)

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