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Bio Chem 501 > Unit 1 > Flashcards

Unit 1 Flashcards

(120 cards)

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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
Mass Spectrometry
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
26
Primary Structure
Sequence of amino acids Peptide bond is planar due to partial double bond (C - N)
27
Secondary Structure
Local 3D configuration
28
Tertiary Structure
Multiple secondary structures together
29
Quaternary Structure
Assembled subunits (tertiary structures)
30
Alpha Helix
3 amino acids per turn Right handed Side chains protrude out
31
of H-bonds in a helix
Number of amino acids - 4
32
#of Turns in a Helix
(# of amino acids) / 4
33
Length of a Helix
(# of turns) x (A length)
34
Beta Sheet
Hydrogen bonds formed between strands Sheets have a twist (not flat) Side chains on alternate sides of the sheet (pleated)
35
Parallel Beta Sheet
Strands run in the same direction Less stable due to H-bonds at an angle
36
Antiparallel Beta sheet
Strands run in opposite directions
37
Tertiary structure motif
Tertiary structures made from arrangements of secondary structures Smaller tertiary units make bigger tertiary structures
38
Source of protein stability
Hydrophobic effect
39
Why do proteins have a size limit
More efficient to build large structures from lots of small ones Error rate of protein synthesis is 1 mistake per 10,000 amino acids
40
Fibrous Proteins
Highly extended Exhibit repeating structure
41
Fibrous Proteins Ex
Keratin, collagen
42
Globular Proteins
Compact Globe shaped
43
Heme Binding Iron
Porphyrin ring provides 4 N ligands to iron (helps stabilize Fe2+) Protein fold stabilizes Fe2+ (binds O2)
44
R to T Change
Oxygen binding moves the histidine → pulls on the helix → changes to R state
45
Oxygen + R State
Oxygen binds more strongly to R state Stabilizes R state
46
Kd
concentration when 50% of the ligand is bound
47
Myoglobin
Not suitable as an oxygen transporter Binds oxygen too tightly Monomer (no 4° structure)
48
Hemoglobin
Tetramer Blood transporter 4 binding sites for oxygen
49
Cooperativity
Binding of the first molecule allows subsequent molecules to bind more tightly Subunits coordinate with each other
50
CO2 + Hemoglobin
CO2 binds to amino end of terminal amino acid
51
H+ and Hemoglobin
H+ binds to side chains
52
Bohr Effect
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
BPG Binding
BPG binds in the cavity between the subunits in the T state
54
BPG + Affinity
BPG lowers binding affinity of hemoglobin for oxygen Stabilizes the T state
55
Properties of Enzymes
Usually protein Incredible catalysts Highly specific Provide control over metabolic processes 3D structure is important for activity Essential for Life
56
Enzymes Complementary to
The TS (Transition State)
57
Acid Base Catalysis
Enzyme provides additional functional groups that help in catalysis once the substrate is bound General acids and bases are contributors
58
Covalent Catalysis
Formation of covalent bond between enzyme and substrate Bond must break in order to release product/regenrate enzyme
59
Metal Ion Catalysis
Positive metal ions stablize negative transition states
60
Fetal Hemoglobin
Lower affinity for BPG Higher affinity for O2 Mother must have more R State
61
Catalytic efficiency
Kcat/Km
62
Enzymes controlled by
Equilibrium constant
63
Chymotrypsin: Ser
Covalent catalysis
64
Chymotrypsin: His
General acid-base catalysis
65
Chymotrypsin: Oxyanion Hole
Lowers Ea by stabilizing oxyanion in TS
66
Chymotrypsin: Hydrophobic pocket
Substate binding and specificity
67
Regulatory enzymes
Must exhibit decreased or increased activity in response to signals
68
Allosteric Enzymes
Change shape Non MM Catalytic and regulatory subunits
69
Regulatory subunit
Binds modulator --> conformation change --> enzyme more active
70
Catalytic subunit
Binds the substrate
71
Feedback inhibition
Product shuts down its own synthesis by negatively regulating an enzyme in the synthesis pathway
72
Covalently Modified enzymes
Regulatory compounds are covalently attached in a reversible matter
73
Zymogens
Made as inactive precursors that need to be cleaved to become active
74
Reversible inhibition
Small molecules that bind in or close to active site
75
Competitive Inhibition
Inhibitor binds to free enzyme Inhibitor competes for active site Affects Km
76
Uncompetitive Inhibition
Inhibitor binds to ES complex Km and Vmax affected equally
77
Mixed Inhibition
Mixture of competitive and noncompetitive Bind to active site or ES complex Affects all parameters unequally
78
Inhibition Y Int
1/Vmax
79
Inhibition X Int
-1/Km
80
Irreversible inhibition
Covalently attach to enzyme Covalent modification of the active site
81
Fatty acids
Carboxyl head (polar) Aliphatic tail (hydrocarbon chain) Named based on # of carbons
82
Saturated fatty acids
Solid at room temp Higher melting point than unsaturated
83
Unsaturated fatty acids
Kink from double bond interferes with packing Lower MP
84
Hydrogenation
Add H across double bond (increase MP)
85
Chymotrypsin Step 1
Substrate binds to hydrophobic pocket
86
Chymotrypsin Step 2
Histidine acts as a general BASE to activate a serine OH group
87
Chymotrypsin Step 3
A serine alkoxide ion attacks a carbonyl carbon of the substrate, forming a covalent acyl bond between enzyme and substrate.
88
Chymotrypsin Step 4
A tetrahedral transition state involving an oxyanion is stabilized by the oxyanion hole
89
Chymotrypsin Step 5
Histidine acts as a general acid to protonate an amide nitrogen. The peptide bond is broken and the first product dissociates.
90
Chymotrypsin Step 6
Water enters the active site
91
Chymotrypsin Step 7
Histidine acts a general base to convert water into a hydroxide ion
92
Chymotrypsin Step 8
A hydroxide ion attacks the acyl bond between substrate and enzyme
93
Chymotrypsin Step 9
A tetrahedral transition state involving an oxyanion is stabilized by the oxyanion hole
94
Chymotrypsin Step 10
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
Why triacylglycerols are good for the energy storage
Highly reduced Provide 2X energy as cards Dehydrated (less space than carbs)
96
Disadvantage of triacylglycerols
Metabolized more slowly than carbs
97
Glycerophospholipids
Phospho group - polar head group Glycerol 3 phosphate = backbone 2 x fatty acids
98
Sphingolipids
Backbone = sphingosine 1 x fatty acid Amide linkage Can have chains of sugars
99
How lipids can be converted into signaling molecules
Prostaglandin = derivative of glycerophospholipids Enzymes break bonds and release acid Acid is modified by enzymes
100
Sterols
Alkyl tail and polar head Steroids derived from cholesterol
101
Hormones
Derived from steroid nucleus of cholesterol No tail More hydrophilic
102
Membrane compartments
ER Nucleus Mitochondria Granules
103
Liposomes
Bilayers wrap around to form continuous, spherical particles
104
Dynamics
Uncatalyzed transbilayer (flip flop) is very slow Uncatalyzed lateral diffusion is very fast
105
Fluidity in membranes
High temp → decrease unsaturated fatty acids Low temp → increase unsaturated fatty acids
106
Hydrogen Bonding
Longer and weaker bond than covalent bonds, prefer 180° angle and 1.8 A distance
107
Myoglobin
Oxygen storage protein
108
Reversible Inhibition
Inhibition of enzyme activity by small molecules
109
Irreversible Inhibition
Covalent modification of enzymes to permanently inhibit their activity
110
Peripheral Membrane Proteins
Proteins that are loosely associated with the membrane
111
Integral membrane proteins
Tightly associated with membrane Require detergent to remove
112
Beta Barrel
Hydrophobic part faces bilayer Hydrophilic part lines pore Facilitated diffusion
113
Passive transport
Diffusion along a gradient No energy required
114
Passive transport types
Simple Facilitated
115
Simple diffusion
Diffusion along a membrane No protein
116
Facilitated diffusion
Requires protein carrier Channels (pores or 1 gate) Passive transporters (2 gates)
117
Active transport
Against the gradient Requires energy
118
Active transport types
Primary Secondary
119
Primary transport
Requires atp Ion pumps
120
Secondary transport
Requires existing gradient Gradient drives cotransport

Bio Chem 501 (4 decks)

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