Unit 1 Flashcards
H-H Equation
pH = pKa + log (A- / HA)
Kw Equation
10^-14 = (H+) x (OH-)
pKa > pH
Protonated
Main Cell Parts (4)
Cytoplasm
Plasma membrane
DNA
Ribosomes
Free Energy Equation
ΔG = ΔH - TΔS
Rate Law
Rate (Product) = k [Reactants]
What is Keq
Keq = (kforward / kreverse)
How far a reaction proceeds in a net direction until equilibrium is reached
RNA World Hypothesis
Life may have started with a self-replicating RNA
Why is RNA possibly the start of life
RNA is a carrier of genetic info
RNA is a catalyst
Phosphate Buffer
Ionization is important
Buffer important for maintaining pH in cells
Decent butter (5.86 to 7.86)
Bicarbonate
Buffer important for maintaining pH in blood
Equilibrium with CO2 (g)
Isoelectric Point
pH where net charge = 0
How does a peptide bond form
Condensation Rxn
Middle amino acids lose their amino and carboxyl ends
Post Translational modification
After a protein is made in the cell, it can be chemically modified by enzymes
Enzymes that modify proteins recognize specific target peptide sequences
What proteins are detected by UV
Tryptophan
Tyrosine (inefficient)
Ion Exchange Chromatography
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
Remove protein from ion exchange chromatography
Change the salt conditions
Size Exclusion Chromatography
Porous column = molecular sieve
Smaller molecules get stuck in pores
Largest molecules come off first, smallest molecules are last
Affinity Chromatography
Protein interacts with ligand and is captured
Unwanted proteins come off first
Remove protein from affinity chromatography
Use excess free ligand
Specific activity
Specific activity = purity of protein
Specific activity = (activity / total protein)
Electrophoresis
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
SDS Page
Codes all proteins with a negative charge
Unfolds proteins for constant shape
Detergent
Isoelectric Focusing
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
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
Primary Structure
Sequence of amino acids
Peptide bond is planar due to partial double bond (C - N)
Secondary Structure
Local 3D configuration
Tertiary Structure
Multiple secondary structures together
Quaternary Structure
Assembled subunits (tertiary structures)
Alpha Helix
3 amino acids per turn
Right handed
Side chains protrude out
of H-bonds in a helix
Number of amino acids - 4
of Turns in a Helix
(# of amino acids) / 4
Length of a Helix
(# of turns) x (A length)
Beta Sheet
Hydrogen bonds formed between strands
Sheets have a twist (not flat)
Side chains on alternate sides of the sheet (pleated)
Parallel Beta Sheet
Strands run in the same direction
Less stable due to H-bonds at an angle
Antiparallel Beta sheet
Strands run in opposite directions
Tertiary structure motif
Tertiary structures made from arrangements of secondary structures
Smaller tertiary units make bigger tertiary structures
Source of protein stability
Hydrophobic effect
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
Fibrous Proteins
Highly extended
Exhibit repeating structure
Fibrous Proteins Ex
Keratin, collagen
Globular Proteins
Compact
Globe shaped
Heme Binding Iron
Porphyrin ring provides 4 N ligands to iron (helps stabilize Fe2+)
Protein fold stabilizes Fe2+ (binds O2)
R to T Change
Oxygen binding moves the histidine → pulls on the helix → changes to R state
Oxygen + R State
Oxygen binds more strongly to R state
Stabilizes R state
Kd
concentration when 50% of the ligand is bound
Myoglobin
Not suitable as an oxygen transporter
Binds oxygen too tightly
Monomer (no 4° structure)
Hemoglobin
Tetramer
Blood transporter
4 binding sites for oxygen
Cooperativity
Binding of the first molecule allows subsequent molecules to bind more tightly
Subunits coordinate with each other
CO2 + Hemoglobin
CO2 binds to amino end of terminal amino acid
H+ and Hemoglobin
H+ binds to side chains
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
BPG Binding
BPG binds in the cavity between the subunits in the T state
BPG + Affinity
BPG lowers binding affinity of hemoglobin for oxygen
Stabilizes the T state
Properties of Enzymes
Usually protein
Incredible catalysts
Highly specific
Provide control over metabolic processes
3D structure is important for activity
Essential for Life
Enzymes Complementary to
The TS (Transition State)
Acid Base Catalysis
Enzyme provides additional functional groups that help in catalysis once the substrate is bound
General acids and bases are contributors
Covalent Catalysis
Formation of covalent bond between enzyme and substrate
Bond must break in order to release product/regenrate enzyme
Metal Ion Catalysis
Positive metal ions stablize negative transition states
Fetal Hemoglobin
Lower affinity for BPG
Higher affinity for O2
Mother must have more R State
Catalytic efficiency
Kcat/Km
Enzymes controlled by
Equilibrium constant
Chymotrypsin: Ser
Covalent catalysis
Chymotrypsin: His
General acid-base catalysis
Chymotrypsin: Oxyanion Hole
Lowers Ea by stabilizing oxyanion in TS
Chymotrypsin: Hydrophobic pocket
Substate binding and specificity
Regulatory enzymes
Must exhibit decreased or increased activity in response to signals
Allosteric Enzymes
Change shape
Non MM
Catalytic and regulatory subunits
Regulatory subunit
Binds modulator –> conformation change –> enzyme more active
Catalytic subunit
Binds the substrate
Feedback inhibition
Product shuts down its own synthesis by negatively regulating an enzyme in the synthesis pathway
Covalently Modified enzymes
Regulatory compounds are covalently attached in a reversible matter
Zymogens
Made as inactive precursors that need to be cleaved to become active
Reversible inhibition
Small molecules that bind in or close to active site
Competitive Inhibition
Inhibitor binds to free enzyme
Inhibitor competes for active site
Affects Km
Uncompetitive Inhibition
Inhibitor binds to ES complex
Km and Vmax affected equally
Mixed Inhibition
Mixture of competitive and noncompetitive
Bind to active site or ES complex
Affects all parameters unequally
Inhibition Y Int
1/Vmax
Inhibition X Int
-1/Km
Irreversible inhibition
Covalently attach to enzyme
Covalent modification of the active site
Fatty acids
Carboxyl head (polar)
Aliphatic tail (hydrocarbon chain)
Named based on # of carbons
Saturated fatty acids
Solid at room temp
Higher melting point than unsaturated
Unsaturated fatty acids
Kink from double bond interferes with packing
Lower MP
Hydrogenation
Add H across double bond (increase MP)
Chymotrypsin Step 1
Substrate binds to hydrophobic pocket
Chymotrypsin Step 2
Histidine acts as a general BASE to activate a serine OH group
Chymotrypsin Step 3
A serine alkoxide ion attacks a carbonyl carbon of the substrate, forming a
covalent acyl bond between enzyme and substrate.
Chymotrypsin Step 4
A tetrahedral transition state involving an oxyanion is stabilized by the
oxyanion hole
Chymotrypsin Step 5
Histidine acts as a general acid to protonate an amide nitrogen.
The peptide bond is broken and the first product dissociates.
Chymotrypsin Step 6
Water enters the active site
Chymotrypsin Step 7
Histidine acts a general base to convert water into a hydroxide ion
Chymotrypsin Step 8
A hydroxide ion attacks the acyl bond between substrate and enzyme
Chymotrypsin Step 9
A tetrahedral transition state involving an oxyanion is stabilized by the oxyanion hole
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.
Why triacylglycerols are good for the energy storage
Highly reduced
Provide 2X energy as cards
Dehydrated (less space than carbs)
Disadvantage of triacylglycerols
Metabolized more slowly than carbs
Glycerophospholipids
Phospho group - polar head group
Glycerol 3 phosphate = backbone
2 x fatty acids
Sphingolipids
Backbone = sphingosine
1 x fatty acid
Amide linkage
Can have chains of sugars
How lipids can be converted into signaling molecules
Prostaglandin = derivative of glycerophospholipids
Enzymes break bonds and release acid
Acid is modified by enzymes
Sterols
Alkyl tail and polar head
Steroids derived from cholesterol
Hormones
Derived from steroid nucleus of cholesterol
No tail
More hydrophilic
Membrane compartments
ER
Nucleus
Mitochondria
Granules
Liposomes
Bilayers wrap around to form continuous, spherical particles
Dynamics
Uncatalyzed transbilayer (flip flop) is very slow
Uncatalyzed lateral diffusion is very fast
Fluidity in membranes
High temp → decrease unsaturated fatty acids
Low temp → increase unsaturated fatty acids
Hydrogen Bonding
Longer and weaker bond than covalent bonds, prefer 180° angle and 1.8 A distance
Myoglobin
Oxygen storage protein
Reversible Inhibition
Inhibition of enzyme activity by small molecules
Irreversible Inhibition
Covalent modification of enzymes to permanently inhibit their activity
Peripheral Membrane Proteins
Proteins that are loosely associated with the membrane
Integral membrane proteins
Tightly associated with membrane
Require detergent to remove
Beta Barrel
Hydrophobic part faces bilayer
Hydrophilic part lines pore
Facilitated diffusion
Passive transport
Diffusion along a gradient
No energy required
Passive transport types
Simple
Facilitated
Simple diffusion
Diffusion along a membrane
No protein
Facilitated diffusion
Requires protein carrier
Channels (pores or 1 gate)
Passive transporters (2 gates)
Active transport
Against the gradient
Requires energy
Active transport types
Primary
Secondary
Primary transport
Requires atp
Ion pumps
Secondary transport
Requires existing gradient
Gradient drives cotransport
