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midterm notes.

oo3 05/12/08 11:07:49 AM

I. Introduction to biomolecules
A. Functional groups
1. hydroxyl
a) R-OH
2. carbonyl
a) R-CO-R
b) R-CO-H
3. carboxyl
a) R-COOH
4. Ether
a) R-O-R
5. Ester
a) R-COO-R
6. sulfhydryl (thiol)
a) R-SH
7. disulfide
a) R-SS-R
8. thioester
a) R-COSH
9. phosphoryl
a) R-POO--OH
10. amino
a) R-N-RR
11. amide (amido)
a) R-CO-NHR
B. Isomers
1. structural
a) differ in bonding sequence
2. stereoisomers
a) diastereomer
(1) non mirror images
b) enantiomers
(1) non-superimposable mirror images
(2) optically active
(3) distinguished by:
i) D /L
(a) configuration relative to glyceraldehyde
(b) if OH group farthest from top faces right when most oxidized group at top (facing away), then D configuration
ii) R/S
(a) absolute configuration by priority of groups bonded to chiral centre
iii) +/-
(a) direction of rotation of polarized light
C. Structure of biomolecules
1. the 3D arrangement in space
a) important for biological activity
(1) binding substrate to enzyme
b) described by:
(1) configuration
i) spatial arrangement about double bonds or chiral centres
ii) can only be changed by breaking bonds
iii) E/Z, R/S
(2) conformation
i) spatial arrangement of groups that are free to assume different positions without breaking bonds
ii) chair/boat in cyclohexane
2. reactivity of biomolecules
a) result of their functional groups 1
2. reactivity of biomolecules
midterm notes.oo3 05/12/08 11:07:49 AM

a) result of their functional groups
b) oxidation
(1) loss of electrons, H or addition of O
(2) increased CO, CN bonds; decreased CH
c) reduction
(1) gain of electrons or H, or removal of O
(2) increased CH bonds; decreased CO, CN
D. Gibb's free energy
1. the useful work that may be obtained from a thermodynamic system
2. the change in Gibb's energy (∆G) determines the spontaneity of a given reaction
a) ∆G<0 spontaneous, will proceed until equilibrium is reached, exergonic
b) ∆G>0 non spontaneous, required input of energy to proceed, endergonic
c) ∆G=0 reaction at equilibrium, no change in free energy
3. in biological systems, non-spontaneous reactions are coupled to spontaneous reactions so that they may occur
a) possible since ∆G values for the individual reactions in a pathway are additive
4. ∆G° is the standard change in gibbs energy for a given reaction at [1M] of reactants and products at 298K (25°C)
a) ∆G=∆G°+RT ln([Products]/[Reactants])
(1) R=molar gas constant
(2) T=absolute temperature
b) at equilibrium
(1) ∆G°=–RT ln(Keq)
5. Overall ∆G is related to entropy and enthalpy
a) entropy (∆H)
(1) change in heat of reaction
b) enthalpy (∆S)
(1) change in randomness of system
c) ∆G=∆H-T∆S
II. Water
A. General Properties
1. polar molecule
a) electronegativity difference between O and H creates dipoles
2. 70% of humans by mass
3. polarity causes cohesion (H-bonding) and adhesion (dipole-dipole)
4. limited dissociation
B. H-bonding
1. weak electrostatic attraction between lone pair electrons of O or N (electronegative) and H attached to another electronegative atom
2. H-bonds of short duration (10-12 s)
a) form and break constantly
b) 3.4 H-bonds at a time in liquid phase, 4 in solid
3. gives water high boiling point and heat of vapourization
C. Solvent properties
1. good solvent of polar molecules
a) orients itself to maximize electrostatic attraction to other molecules
b) in solvation, charged particles are surrounded or insulated by water molecules
2. Interactions with biomolecules
a) H-bonding with polar and ionic biomolecules
b) solubility increases with number of polar groups
c) influences amphipathic molecules
(1) amphipathic
i) molecule with polar group and non-polar region
(a) fatty acids
(2) causes formation of aggregates
i) micelles, bilayers
ii) stablilized by H-bonding and hydrophobic tendency to minimize interaction between non-polar regions and water
3. Non-covalent interactions in biomolecules
2
(2) causes formation of aggregates

midterm notes.oo3 ii) stablilized by H-bonding and hydrophobic tendency to minimize interaction between non-polar regions and water 05/12/08 11:07:49 AM

3. Non-covalent interactions in biomolecules
a) critical to structure and function of biomolecules
b) ionic
(1) electrostatic interactions between charged molecules
c) hydrogen bonds
(1) weak electrostatic interactions between lone pair electrons and H atoms
d) Van der Waals forces
(1) non-covalent attractive forces between 2 neutral molecules due to dipoles
i) dipole-dipole
(a) attraction between 2 permanent dipoles
ii) dipole-induced dipole
(a) a transient dipole is induced by a nearby dipole by random attraction of electrons
iii) induced-induced dipoles
(a) transient dipoles formed for very short periods due to random, uneven distribution of electrons
e) hydrophobic
(1) association of non-polar molecules in aqueous solution rather than with water
D. Dissociation of water
1. 2 H O ⇌ H O+ + OH-
2 3
a) Water acts as both a Bronsted-Lowry acid and bsase (amphoteric)
2. dissociation is limited
3. K = [H O+][OH-] = 10-14 M
w 3
4. pH = -log [H+]
E. Weak acids and bases
1. maintain pH in living orgnisms
2. partial ionization allows creation of buffer solutions
a) resist changes in pH by increasing or decreasing ionization due to Le Chatelier's principle
(1) unlike strong acids which ionize completely in solution
3. Henderson Hasselbalch Equation
a) represents the pH of a buffer solution as OH- is added

b) pH=pK + log([A-]/[HA])
a
c) buffer solution is best able to resist pH change when HA is half-ionized
(1) pH=pKa

(2) most buffers have a buffering zone of ± 1 pH on each side of pKa
d) polyprotic acids will have more than one buffering zone
III. Carbohydrates
A. General
1. types
a) monosaccharides
(1) simple sugars
(2) one sugar
(3) single polyhydroxyaldehyde/ketone
(4) glucose, fructose, etc.
b) oligosaccharides
(1) short chains of monosaccharides linked by glycoside bonds
(2) disaccharides:sucrose,lactose
c) polysaccharides
(1) linear or branched chains of monosaccharides
(2) can be linked to lipids or proteins
(3) starch, cellulose
2. function:
a) primary energy source
(1) oxidized to CO2 + H2O + ATP
b) storage form of energy 3
2. function:
a) primary energy source
midterm notes.oo3 (1) oxidized to CO2 + H2O + ATP 05/12/08 11:07:49 AM

b) storage form of energy
(1) Glycogen, starch
c) biosynthesis
d) structural components
(1) cellulose
(2) chitin
e) informational roles
(1) recognition complexes
B. Monosaccharides
1. polyhydroxy aldehyde = aldose
a) glucose
b) most have -ose suffix
c) smallest is glyceraldehyde
2. polyhydroxy ketone = ketose
a) suffix -ulose
b) smallest is dihydroxyacetone
3. Most monosaccharides are in D configuration
4. epimers
a) monosaccharides which differ only in configuration at one chiral carbon
(1) glucose / galactose @ C4
5. monosaccharides can exist in a ring form by forming a hemiacetal or hemiketal by bonding to carboxyl carbon (anomeric)
a) anomers
(1) cyclic monosaccharides can exist in two configurations of the straight chain form
(2) α: OH group on anomeric carbon E to other group on ring, usually C6
(3) ß: OH group on anomeric carbon Z to other group on ring
b) anomers interconvert using straight form as intermediate
c) 5 membered rings:
(1) furanose
d) 6 membered rings:
(1) pyranose
(2) has boat and chair conformations (chair most stable)
i) glucose most stable monosaccharide since it has all non-H substituents in equatorial position of chair conformation
e) if a group is covalently linked to the anomeric carbon's OH, it constitutes a glycosidic bond
6. reducing sugars
a) a sugar is reducing if it has a free carboxyl group in the straight-chain form
b) all monosaccharides are reducing, but not all oligosaccharides
(1) lactose is reducing since it's 1-4 glycosidic bond only occupies one of the two carboxyl groups
(2) sucrose is not reducing because it's 1-2 glycosidic bond occupies both carboxyl groups (bond is to the anomeric carbon of each
constituent monosaccharide)
c) if aldehyde or ketone is reduced to an alcohol, it results in sugar alcohols
(1) glucose -> sorbitol
7. Examples
a) mannose
(1) hexoaldose
(2) pyranose
(3) configuration of highest priority groups after anomeric carbon (in numerical order)
i) up-up-down

(4)

b) glucose
(1) hexoaldose (anomeric carbon C1)
(2) pyranose
4
b) glucose
midterm notes.oo3 (1) hexoaldose (anomeric carbon C1) 05/12/08 11:07:49 AM

(2) pyranose
(3) configuration of highest priority groups after anomeric carbon (in numerical order)
i) down-up-down

(4)

c) galactose
(1) hexoaldose
(2) pyranose
(3) configuration of highest priority groups after anomeric carbon (in numerical order)
i) down-up-up

(4)

d) fructose
(1) hexoketose (anomeric carbon C2)
(2) furanose
(3) configuration of highest priority groups after anomeric carbon (in numerical order)
i) up-down-up (group on C5 is CH2 OH)

(4)

C. Oligosaccharides
1. 2-20 monosaccharides linked via glycosidic bonds
2. disaccharides formed when two monosaccharides bond by the OH on anomeric carbon of one monosaccharide forms an acetal with an OH on
the second monosaccharide by removing an HOH molecule (dehydration synthesis)
3. α or ß configuration of sugar giving anomeric OH determines configuration of resulting glycosidic bond
4. if the chain formed has a free anomeric carbon, that end is called the reducing end (see B.6)
5. oligosaccharides named from non-reducing end towards the reducing end
6. anomeric configuration of reducing end may interconvert
7. Examples
a) maltose
(1) α-D-glucopyranosyl-(1–4)-ß-D-glucopyranose
i) glycoside bond is α
ii) sugar is reducing (1–4 bond)
iii) -syl means the molecule is inside the chain
iv) -ose means the end of the chain is reducing

v)

b) lactose
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v)

midterm notes.oo3 05/12/08 11:07:49 AM

b) lactose
(1) ß-D-galactopyranosyl-(1–4)-ß-D-glucopyranose
i) glycoside bond is ß
ii) sugar is reducing

iii)

c) sucrose
(1) α-D-glucopyransyl-( 1–2)-ß-D-fructofuranoside
i) glycoside bond is α
ii) sugar is non-reducing (both anomeric carbons involved in bonding)
iii) -oside means that fructose has no reducing end

iv)

D. Polysaccharides
1. >20 sugars
2. Classification
a) homopolysaccharides
(1) same sugar residues
i) amylose (D-glucose)
b) heteropolysaccharides
(1) different sugar residues
3. Starch
a) amylose
(1) unbranched glucose polymer
i) α1–4 bonds
ii) 10-1000 residue chains
(a) single chains coil into tight helices
(2) storage form of carbohydrate in plants and fungi
(3) broken down by α-amylase
i) cleaves 1–4 bond between glucoses
b) amylopectin
(1) branched glucose polymer
(2) main chain segments are α1–4 bonds, branches attached with α1–6 bonds
i) 300-600 residues
ii) branches create many non-reducing ends
iii) branched every 20-25 residues
(a) prevents helix formation
(3) broken down by α-amylase (1–4) and debranching enzyme (1–6)
c) glycogen
(1) more highly branched form of amylopectin
i) every 8-10 residues
(2) used as animal storage carbohydrate 6
c) glycogen
(1) more highly branched form of amylopectin
midterm notes.oo3 i) every 8-10 residues 05/12/08 11:07:49 AM

(2) used as animal storage carbohydrate
i) stored in liver and muscle cells
(3) very high number of non-reducing ends allows rapid release of glucose into bloodstream
d) cellulose
(1) structural component of plants
(2) up to 15 000 glucose molecules
i) ß1–4 linked with extensive H-bonding
(a) results in very strong and insoluble structure
(3) ß-glucosidase (cellulase) cleaves ß1–4 bonds
IV. Organic Chemistry Review
A. Reactions
1. oxidation
a) R-OH —> R=O
b) primary alcohol —> aldehyde —> carboxylic acid
c) secondary alcohol —> ketone
2. esterification
a) alcohol/thiol + carboxylic acid —> ester/thioester + HOH
3. reduction
a) aldehyde —[H+]—> primary alcohol
b) ketone —[H+]—> secondary alcohol
c) carboxylic acid —[H]—> aldehyde
4. hemiacetal formation
a) aldehyde + alcohol <—> hemiacetal
5. acetal formation
a) hemiacetal + alcohol —> acetal + HOH
6. aldol condensation
a) 2 aldehydes or ketones —> hydroxyadehyde/ketone
7. acid anhydride
a) 2 carboxylic acids —> acid anhydride
8. amide formation
a) carboxylic acid + ammonia/amine —> amide + HOH
V. 3 Dimensional Structure of Proteins
A. Physiological Roles of Proteins
1. Enzymes
a) biochemical catalysts
2. Storage and transport
3. Cellular structure
4. Mechanical movement
5. Decoding cell information
6. Hormones or hormone receptors
7. Other specialized functions
8. Each protein has specialized structure for specific function
B. General Classes of Proteins
1. Fibrous
a) simple, linear structures
b) structural
2. Globular
a) spherical and soluble
b) enzymes and transport
3. Membrane
a) associated with a membrane
b) receptors, transporters, pumps
C. Protein Conformation and Folding
1. native proteins only marginally stable
2. stabilized by weak interactions
a) greatest number of weak interactions is the most stable conformation (lowest ∆G) 7
C. Protein Conformation and Folding

2. stabilized by weak interactions
midterm notes.oo3 05/12/08 11:07:49 AM

a) greatest number of weak interactions is the most stable conformation (lowest ∆G)
3. native conformation is the single stable folding shape at physiological conditions
4. Folding
a) rapid step-wise process (<1 second)
b) individual secondary structures first, then core condenses to tertiary
c) some protein folding spontaneous, others require chaperone proteins
5. Denaturation
a) disruption of native conformation; loss of biological function
b) energy required only 3-4 H-bond equivalents
c) cooperative process
d) only some proteins can renature
D. 4 Levels of Protein Structure
1. Primary
a) linear sequence of amino acids
(1) no three-dimensional structure
b) defines composition of amino acid
c) sequence presented from N –> C termina
(1) eg. NH3+–MLCDTN–COO-
(2) repeating pattern of N-CR-C-N-CR-C-N in main chain
2. Secondary
a) localized interactions within polypeptide
b) patterns in local conformation due to H-bonds between amide H's and carbonyl O's
c) a region of secondary structure will have a single H-bonding pattern
(1) polypeptide folding is restricted by limited flexibility of peptide bond
d) determinants of allowed secondary structures
(1) favoured conformations of peptide bond
i) CN bond exhibits resonance, restricting rotation
(a) rotation only about N-CR (Phi Φ) and CR-C (Psi Ψ) bonds
i) most conformations prevented by steric interference
ii) allowed conformations graphed on Ramachadran plot
ii) almost all peptide bonds in proteins are trans (E)
(2) optimization of hydrogen bonding potential
i) each peptide bond has both H-bond donor and acceptor
(a) donor: NH group
(b) acceptor: C=O group
e) Structures:
(1) α-helix
i) right-handed
ii) 3.6 residues/turn
(a) H-bonding between C=O and the H-N 4 residues away
iii) stabilized by many H-bonds parallel to axis of helix
iv) entire helix is a dipole
(a) + at N terminus
(b) - at C terminus
(c) all C=O groups point toward C terminus, all NH groups point toward N terminus
(d) dipole communicated to ends through H-bonding
(e) primary structure can stabilize helix by having positive residues at C terminus and negative at N terminus
v) Φ and Ψ angles of each residue similar
vi) primary structure affects helix stability
(a) many positive or negative residues in sequence usually do not form helices due to electrostatic repulsion
(b) residues 3-4 positions apart will be close together in helix
i) positive usually found 3-4 positions from negative residues
(c) proline seldom found in helices due to rigidity (known as helix-breaker)
vii) Amphipathic helix
(a) helix in which hydrophobic residues are on one side of the helix (all 3-4 residues away in primary structure) and hydrophilic on the
opposite side
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midterm notes.oo3 vii) Amphipathic helix 05/12/08 11:07:49 AM

(a) helix in which hydrophobic residues are on one side of the helix (all 3-4 residues away in primary structure) and hydrophilic on the
opposite side
(2) ß-strands and sheets
i) ß-strand
(a) polypeptide chains almost fully extended
ii) ß-sheet
(a) multiple ß-strands arranged side by side with H-bonds between
(b) parallel ß-sheets
i) strands run in the same N –> C termina direction
(c) antiparallel ß-sheets
i) stands run in alternate N–>C termina directions
ii) H-bonding more stable; more perpendicular to chains
(A) antiparallel slightly more stable than parallel
(d) residue R groups project alternately above and below sheet
i) every second R group on the same side
ii) amphipathic ß-sheets have one hydrophobic and one hydrophilic side
(A) can interact with amphipathic α-helices
(3) Turns
i) connect helices and strands
ii) allow peptide chain to fold back on itself
iii) are loops with < 5 residues
iv) ß-turns (reverse turns)
(a) connect different antiparallel ß-strands
3. Tertiary
a) final structure of a single polypeptide
4. Quaternary
a) structure involving multiple polypeptides
(1) multiple subunits joined together
i) may be same type or different polypeptides
(2) held by non-covalent interactions
b) helps stabilize subunits; prolongs life of protein
c) unique active sites at subunit interfaces
d) unique/dynamic function through changes in tertiary and quaternary structure
e) combinations of simpler subunits more efficient than selection for new protein with ideal function
E. Examples of Protein Structure/Function
1. Keratin
a) 2 RH α-helices twisted into LH coil
(1) α-helices associate by hydrophobic interactions
i) each helix has hydrophobic side due to a 7-residue pseudorepeat of hydrophobic residues
b) stabilized by disulfide bonds
(1) more disulfides, greater hardness
i) hair vs. horn
c) forms hair, nails, horns
2. Collagen
a) 25% of human protein
(1) major structural protein that forms skin and tendons
b) 3 LH helical chains coiled into RH triple helix
c) repeats of Gly-X-Y, where X often Proline or Y often hydroxyproline
(1) Gly R group faces inwards; -H is only group small enough to fit inside
(2) hydroxyproline, hydroxylysine
i) formed by hydroxylation reactions with vitamin C cofactor
ii) stabilize collagen
iii) scurvy leads to defective triple helix
(a) humans cannot synthsize vitamin C
3. Silk
a) cocoons, webs
9
3. Silk
midterm notes.oo3 05/12/08 11:07:49 AM

a) cocoons, webs
b) very high strength
c) small amino acids in 6 residue repeat
VI. Protein Function
A. Reversible binding of a protein to a Ligand — Oxygen transport proteins
1. heme prosthetic group
a) non-polypeptide
b) found in both myoglobin and hemoglobin
c) tetrapyrrole ring bound to iron
(1) iron has 4 bonds to tetrapyrrole ring; 2 free bond locations
(2) in Mb and Hb, one position occupied by histidine, the other is free to bond with O 2 , CO, or NO
i) neither Mb and Hb, or heme can bind oxygen alone; only when bonded together
2. Myoglobin (Mb)
a) Structure
(1) monomeric protein
i) globin polypeptide covalently bonded to heme prosthetic group
ii) single oxygen binding site
(a) strong reversible interaction
b) facilitates oxygen transport in peripheral tissue
c) called Oxymyglobin when oxygen-bound
d) Deoxymyoglobin is oxygen-free
e) Oxygen binding curve is hyperbolic with half saturation point ~ .26 kPa
(1) saturation = [pO2 ]/([PO2 ]+P50 )
3. Hemoglobin
a) tetrameric
(1) each globin subunit has own heme group
i) 4 oxygen bonding sites
(2) each subunit similar to single myoglobin protein
b) found in RBCs that transports oxygen from lungs to periphery through blood
(1) 96% sat in arteries, 64% in veins under normal conditions
c) Binding curve
(1) Hb exhibits positive cooperativity
i) O2 affinity increases as more O2 is bound
(a) structural change is initiated when one Hb subunit is bound
i) subunits are tight enough that tertiary change in one subunit, changes conformation of the other 3
ii) oxygen causes subunits to go from tense to relaxed structures
d) allosteric properties
(1) Hb is an allosteric protein
i) it's activity is affected by allosteric effectors that bind at sites separate from the functional site
(a) allosteric activators stabilize R state, shifting equilibrium in R direction
(b) allosteric inhibitors stabilize T state, shifting equilibrium in T direction
ii) 2,3BPG (Bisphospho-D-Glycerate) is an allosteric inhibitor of Hb
(a) is a negatively charged molecule that binds to six positive residues at its receptor
i) fetal Hb has only 5 residues
(A) is less inhibited in order to take oxygen from maternal Hb by having higher affinity
(b) lowers oxygen affinity
i) allows oxygen to be transferred from Hb to Mb
e) Bohr effect
(1) Hb O2 affinity increases with pH

(2) CO2 reduces pH in blood, lowering affinity, releasing O2 into tissue
4. Sickle Cell Anemia
a) Hb mutation of E –> V
b) forms fibres at low partial oxygen pressure which block capillaries
c) selective advantage in malaria endemic areas
10
(1) malaria lowers pH in infected cells, causing fibres and spleen destroys infected cells
c) selective advantage in malaria endemic areas
midterm notes.oo3 05/12/08 11:07:49 AM

(1) malaria lowers pH in infected cells, causing fibres and spleen destroys infected cells
VII. Enzymes
A. Overview
1. enzymes are required for life
a) efficiently and selectively catalyze chemical reactions required for life
b) most biomolecules too stable to transform quickly enough for life
2. practical applications
a) genetic disorders involve enzyme deficiency
b) biomarkers
c) drugs designed to influence enzymes
d) commercial/industrial
3. most enzmes are proteins
a) some RNA molecules are the exception
4. many enzymes have full activity alone
a) others require co-factors (inorganic ions) or co-enzymes (organic/ vitamins)
(1) a tightly associated co-enzyme or co-factor is called a prosthetic group
heme in Hb and Mb
b) Apoenzyme
(1) enzyme which does not have a required co-factor/enzyme
c) Holoenzyme
(1) Apoenzyme that has aquired a required co-factor/enzyme
B. Classification
1. Oxidoreductases
a) transfer of electrons
2. Transferases
a) group transfer reactions
3. Hydrolases
a) hydrolysis (transfer of functional groups to water)
4. Lyases
a) addition of groups to double bonds
b) formation of double bonds
5. Isomerases
a) transfer of groups within molecules to get isomeric forms
6. Ligases
a) formation of C-C, C-S, C-O, C-N bonds by condensation with ATP cleavage
C. Function
1. lower activation energy of the transition state by using alternate reaction pathway
a) increase rate without changing equilibrium
(1) ∆G remains the same, ∆G‡ (activation energy) decreased
b) relationship between rate constant and activation energy is inverse and exponential
(1) rate enhancements can be of the order of 107
2. not consumed by reaction
3. compared to chemical catalysts:
a) faster
b) milder conditions
c) greater specificity
d) can be regulated
4. catalyse the interconversion of substrate and product
5. active site
a) portion of the enzyme that binds the substrate, forming ES complex
6. some enzymes limited by diffusion since reaction proceeds faster than encounters between enzyme and substrate
a) circe effect
(1) some enzymes even faster than diffusion limits due to electrostatic attraction of substrate molecules
D. Modes of enzymatic catalysis - how activation energy is reduced
1. Binding effects
a) substrate binding 11
D. Modes of enzymatic catalysis - how activation energy is reduced
1. Binding effects
midterm notes.oo3 05/12/08 11:07:49 AM

a) substrate binding
(1) not only provides substrate specificity, but increases rate by proximity effect
i) enzyme gathers and positions substrates
(a) reduces entropy
(b) desolvates substrate
(c) distorts substrate
(d) aligns substrate with enzyme
(e) induced fit
b) transition-state stabilization
(1) enzyme is complementary to transition state (not substrate)
i) must be similar enough to substrate to be specific, but different enough to promote reaction
(2) transition state analogues
i) antibody formed against transition state analogue may act as an enzyme to bind substrate and push towards transition state
2. Chemical effects
a) acid/base catalysis
(1) polar, ionizable residues act as proton donors/acceptors to catalyse reaction
i) same mechanism as acid/base catalysed reactions in organic chemistry
b) covalent catalysis
(1) substrate bonds covalently to enzyme forming reactive intermediate which participates in a second reaction to restore enzyme and form
product
E. Enzyme Kinetics
1. Velocity
a) V=∆[P]/∆t
2. Influencing factors
a) Temperature and pH
(1) bell shaped curve about optimum pH/temperature
b) Enzyme concentration
(1) linear relationship
3. Initial velocity (V0 )
a) velocity at the beginning of reaction; prior to product formation
b) dependant on substrate concentration
c) ES —> E + P must be rate-determining step of reaction for M-M approximation
(1) V0 =[ES]k2
d) steady-state approximation
(1) ES formation=ES breakdown
e) Michaelis-Menten equation
(1) V0 = {(Vmax)[S]}/{Km+[S]}

i) Vmax= maximum initial velocity
(a) dependant on enzyme concentration/velocity
i) enzyme fully saturated with substrate
ii) Km= substrate concentration at 1/2 maximum initial velocity
4. comparison of enzyme activities
a) Kcat=Vmax/[E]t
(1) number of substrate molecules converted to product per unit time in saturating conditions
5. Lineweaver-Burk plot
a) double-reciprocal analysis of kinetic data

(1) V -1=(K /V -1 -1
0 m max)([S] ) + Vmax

12
a) double-reciprocal analysis of kinetic data

(1) V -1=(K /V -1 -1
midterm notes.oo3 0 m max)([S] ) + Vmax 05/12/08 11:07:49 AM

b)

c) Reversible Inhibitors
(1) Compound that binds to an enzyme and interferes with its activity
i) non-covalent interactions
(2) Competitive
i) Binds to free enzyme E; competes with S for E
(a) only either I or S can bind with E at a given time
ii) usually resembles substrate
iii) Vmax is the same; Km is increased
(a) inhibition can be overcome by increasing [S]

iv)

(3) Uncompetitive
i) binds to ES, not E
ii) Vmax decreased due to production of ESI
(a) not all ES will immediately form E + P
(b) takes longer for P to separate from E
iii) Km decreased
(a) since [ES] decreased due to production of ESI, from LCP, apparent substrate affinity of enzyme increases
i) equilibrium shifts towards ES

13

iv)
iii) m
(a) since [ES] decreased due to production of ESI, from LCP, apparent substrate affinity of enzyme increases
midterm notes.oo3 i) equilibrium shifts towards ES 05/12/08 11:07:49 AM

iv)

(4) Mixed inhibitors
i) binds to both E and ES
(a) I does not bind to active site
ii) Vmax decreases due to formation of 2 non-productive complexes EI and ESI
iii) Km does not change
actually, only true if rates of E + I —> EI and ES + I —> ESI are the same, which is non-competitive inhibition. Plot below is of mixed inhibition. By
above definition, each line should have the same x-intercept

iv)

d) Irreversible Inhibition
(1) inhibitors that form stable covalent bonds with enzyme or disrupt essential functional group of the enzyme
(2) Suicidal Inactivators
i) initially unreactive, but after first steps of catalysis, are converted to reactive species that inactivates the enzyme
ii) form of irreversible inhibition using normal catalytic process
F. Serine Proteases
1. cleave peptide bonds in protein substrates
2. digestive enzymes
a) trypsin
b) chymotrypsin
c) elastase
3. covalent and acid-base catalysis
4. stored as inactive zymogens that are activated by proteolysis
G. Regulation of Enzymes
1. Regulation of availability
a) location, rates of synthesis and degradation
2. Regulation of activity
a) covalent modification
(1) phosphorylation, methylation, glycosylation
(2) interconvertible enzymes
(3) catalyzed by converter enzymes 14
a) covalent modification

midterm notes.oo3 (2) interconvertible enzymes 05/12/08 11:07:49 AM

(3) catalyzed by converter enzymes
i) controlled by allosteric modulators
b) allosteric modification
(1) binding of a regulatory molecule
3. Points of regulation
a) processes usually regulated at rate-limiting step
(1) negative feedback inhibition
(2) conserves material and prevents accumulation of intermediates
4. Allosteric enzymes
a) regulated by interaction with metabolic intermediates
(1) modulators
i) activators and inhibitors
(a) activators and substrates bind only to the R state
(b) inhibitors bind only to T state
(2) bind non-covalently
b) usually quaternary structures
c) do not obey M-M kinetics; sigmoidal curves
d) PFK-1
(1) Activated by ADP
(2) inhibited by PEP
VIII. Lipids
A. General
1. hydrophobic
2. low molecular weight relative to nucleic acids and proteins
B. Biological Functions
1. Energy storage
2. Structural
a) cell membranes
3. biochemical signals
a) steroid hormones
4. enzyme cofactors
5. pigments
C. Triacylglycerols (Triglycerides)

1.

2. storage lipids in plants and animals
3. glycerol with 3 fatty acids bonded by ester bonds
a) each fatty acid usually different
(1) even number of atoms
(2) between 12-24 carbon atoms long
b) saturated fatty acids have no double bonds
c) unsaturated have 1-3 double bonds
(1) conjugated double bonds rare
4. melting point
a) related to intermolecular forces
b) increases with length of fatty acid chains
c) decreases with number of double bonds
(1) kinks in chains make less efficient packing; lower IMF
5. Fatty acid numeric nomenclature: 15
c) decreases with number of double bonds
midterm notes.oo3 (1) kinks in chains make less efficient packing; lower IMF 05/12/08 11:07:49 AM

5. Fatty acid numeric nomenclature:
a) 18:2(∆9,12)
(1) 18 Carbon
(2) 2 double bonds at C9 and C12
D. Lipids versus Carbohydrates
1. Lipids store more energy, but slower to release
2. Lipids release water when broken down, polysaccharides require water to break down
E. Structural Lipids
1. form cell membranes that separate aqueous compartments
2. 2 sets of amphipathic lipids with polar headgroups and hydrophobic tails form bilayers
a) composed of:
(1) backbone
(2) hydrocarbon tails; fatty acids
(3) polar headgroup
(4) Examples
i) phospholipids
(a) glycerophospholipids
i) glycerol backbone
ii) PO4+alcohol head
(b) sphingophospholipids
i) sphingosine backbone
ii) PO4+choline or other head
ii) glycolipids
(a) Sphingoglycolipids
i) sphingosine backbone
ii) mono or oligosaccharide head
(b) Galactolipids (sulfolipids)
i) glycerol backbone
ii) mono or disaccharide and SO4 head

iii)

3. Glycerophospholipids
a) usually in animal cells
b) glycerol backbone
c) C1 usually saturated fatty acid 16-18
d) C2 usually longer unsaturated 18-20
e) C3 Phosphatditic acid derivative
(1) PO4 group with phosphodiester bond to head group constituent
i) Phosphaditic acid
(a) -H
(b) -1 charge
PO4 group has 1- charge + charge of head group
ii) Phosphatidylethanolamine 16
(b) -1 charge
midterm notes.oo3 PO4 group has 1- charge + charge of head group 05/12/08 11:07:49 AM

ii) Phosphatidylethanolamine

(a) -CH -CH -N+H
2 2 3
(b) OH from alcohol forms part of PO4 group
(c) 0 charge
iii) Phosphatidylcholine

(a) -CH -CH -N+(CH )
2 2 33
(b) 0 charge
iv) Phosphatidylserine
(a) -CH -CH(COO– )-NH3+
2
(b) 1- charge
v) Phosphatidylglycerol
(a) -CH2 -CH(OH)-CH2 -OH
(b) 1- charge
vi) phosphatidylinositol-4,5-bisphosphate
(a) -diphosphopyranose
(b) 4- charge
vii) Cardiolipin
(a) phosphatidyl-glycerol
(b) -PO4 -glycerol with 2 ester-bonded fatty acids
(c) 2- charge
4. Galactolipids and Sulfolipids
a) plant membranes use galactose and sulfate instead of phosphate
b) phosphate often a limiting nutrient
5. Ether-linked lipids
a) ether bonds are more stable and more resistant to lipases
b) found in archaebacteria
(1) live in extreme environments
(2) often as tetraether lipids

(3)

(4) diphytanyl groups twice as long as typical fatty acids in membranes
i) one tetraether lipid spans entire thickness of membrane as opposed to halfway in plant and animal cells
6. Sphingolipids
a) Ceramide
(1) -H
(2) neutral
b) Sphingomyelin
(1) -phosphocholine

(2) -PO -CH -CH -N+(CH )
3 2 2 33
(3) 1+ charge
c) Neutral glycolipids
(1) glucosylcerebroside
i) found in plasma membrane
ii) -glucose
d) Lactosylceramide 17
(1) glucosylcerebroside

midterm notes.oo3 ii) -glucose 05/12/08 11:07:49 AM

d) Lactosylceramide
(1) -Di, tri, or tetrasaccharide
(2) -Glu-Gal
e) Ganglioside GM2
(1) -complex olicosaccharide
(2) contains sialic acid
(3) negative charge
f) Glycosphingolipids found as RBC antigens
7. Phospholipid and Sphingolipid degradation
a) recycled by lysosome enzymes
b) lipases sever ester bonds linking backbone to chains
c) glycosidases cleave sugar units apart
8. Sterols
a) 4 fused carbon rings
(1) 1 - 5C ring
(2) 3 - 6C rings
b) Structural lipid form
(1) long alkyl chain on C17
c) detergent form
(1) charged headgroup
(2) amphipathic molecule
d) steroid hormones
(1) no long chains
(2) no charged groups
(3) polar substituents on C17
9. Vitamins
a) Vitamin D

(1)

(2) produced in skin from UV exposure of 7-dehydrocholesterol
(3) hydroxylated in kidney and liver to 1,25-dihydroxyvitamin D3
i) regulates calcium ion uptake in intestines
(a) deficiency leads to ricketts
b) Vitamin A (retinol)

18
(1)
b) Vitamin A (retinol)
midterm notes.oo3 05/12/08 11:07:49 AM

(1)

(2) produced form dietary ß-carotene
i) made from isoprene units
(a) CH2 =C(CH3 )-CH=CH2
(3) oxidized to cis-retinal
i) visual pigment
(a) when exposed to light, becomes trans-retinal
ii) oxidized to retinoic acid
(a) hormone
c) Vitamin E

(1)

(2) antioxidant
i) reacts with free oxygen radicles to prevent damage to lipids
(3) highly soluble in lipids
d) Vitamin K

(1)

(2) prothrombin activation in blood clotting
e) Ubiquinone

(1)

(2) electron transporter in mitochondrial membrane
(3) oxidized (quinone) and reduced (quinol) both highly soluble in lipid membrane
19
midterm notes.oo3 (2) electron transporter in mitochondrial membrane 05/12/08 11:07:49 AM

(3) oxidized (quinone) and reduced (quinol) both highly soluble in lipid membrane
i) can shuttle electrons and protons from one side of membrane to the other
IX. Membranes and Transport
A. Lipid aggregates
1. Micelle
a) spherical structure with hydrophobic interior and hydrophilic exterior
(1) formed from fatty acids and detergents
i) chain has smaller cross-section than head
2. Bilayer
a) flat double-layer with hydrophilic exterior and hydrophobic core
(1) formed from glycerophospholipids and sphingolipids
i) similar chain and head cross-section
B. Functions of membranes
1. physically separate cells from external medium and organelles from cytoplasm
a) important to maintain concentrations of biomolecules
b) segregation of proteins
2. facilitate transport of substrates and ions
3. sites of energy conversion in living cells
a) mitochondria, chloroplasts, bacterial plasma membrane
4. changes of electrical potential are basis of nervous system
5. cell-cell interaction
6. contain hormonal and other receptors
C. Cellular membranes
1. edges of bilayers are unstable
a) tend to form membrane vesicles
2. cellular membranes contain lipids and membrane proteins
a) both freely diffuse in the plane of the membrane
3. biomolecular reactions can be more efficient in membrane due to higher probability of collision
4. lipid diffusion is slow across membrane
a) diferent composition on each side
b) accelerated by flippase enzymes
5. phase transition temperature
a) in a pure bilayer, below phase transition temperature, lipids are in paracrystalline state, above in fluid state; intermediate, lateral diffusion
but partially ordered
b) temperature depends on fatty acid composition of phospholipids
c) in biological membranes (not pure bilayer) uneven phases across membrane
(1) lipid rafts formed by sphingolipids and cholesterol
i) ordered lipid surrounded by disordered fluid
ii) stabilized by cholesterol ring interactions
iii) attachment points for peripheral membrane proteins
(a) anchored by covalently-attached acyl chains or glycosylated phosphoinositol derivatives (GPIs)
6. Peripheral and integral membrane proteins
a) peripheral
(1) attached to membrane by covalently-linked lipid anchors or non-covalent bonds with other proteins
i) GPI anchored proteins are always outside cell
ii) fatty acyl or prenyl anchors are always inside cell
b) integral
(1) immersed in the membrane
(2) can be extracted with detergents
(3) 2 structural types
i) α-helical bundles
ii) ß-barrels
iii) length of transmembrane proteins determined by thickness of bilayer
(4) charged residues in proteins mostly outside the membrane or in active site
i) apolar residues inside hydrophobic slab of membrane
ii) Try and Tyr at head-tail interface
20
(4) charged residues in proteins mostly outside the membrane or in active site
midterm notes.oo3 i) apolar residues inside hydrophobic slab of membrane 05/12/08 11:07:49 AM

ii) Try and Tyr at head-tail interface
D. Membrane Fusion
1. Central to many biological processes
a) synaptic junctions
(1) vesicle containing neurotransmitters approaches membrane of receptor
(2) SNAP and SNARE proteins bind together to draw membranes together
(3) void formed and fusion pore allows vesicle contents to enter
E. Membrane diffusion
1. diffusion influenced by both concentration and electrical potential gradients
2. ∆μXm+=m∆Ψ–(2.3RT/F)•log([C in ]/[Cout ])
∆Ψ is normally out–in, inside is negative and outside is positive, so ∆Ψ will also be positive. However when measuring action potentials in neurons, usually
in-out is used.
a) ∆μH+=∆Ψ–(60 mV)∆pH(in-out)

For protons m=1 and log [H+in]–log[H+out] = ∆pH

b) ∆μXm+= –∆G/F
(1) if ∆μXm+ > 0 then since ∆G < 0 diffusion will occur down electrochemical gradient

c) ∆μXm+= electrochemical potential difference
d) F= Faraday constant
e) ∆Ψ = membrane potential
f) m = charge of particle diffusing
F. Membrane Transporters
1. lower activation energy barrier by replacing substrate hydration shell with polar groups along path
2. Channels
a) membrane pores that can only transport down electrochemical gradient (passive)
b) very high conductance
(1) bind substrate weakly
(2) no saturation behaviour
3. Carriers
a) rate-limiting step of substrate binding to protein
(1) Michaelis-Menten equation
(2) lower rate of transport
b) both active and passive transport
c) Example: glucose transporter in erythrocytes
(1) passive carrier
plasma glucose concentration higher than within RBCs
(2) V0 =(Vmax•[S]out )/(Kt+[S]out )
(3) polar sidechains H-bond with glucose in inside of pore
i) pore constructed from several helices
4. Cotransport
a) two substrates pass through transporter at the same time
b) Symporter
(1) substrates pass through in same direction
c) Antiporter
(1) substrates pass through in opposite direction
(2) electroneutral ion exchange prevents change in membrane potential
(3) electrogenic exchange uses membrane potential to drive active ion transport
5. Types of membrane transport processes
a) Active (against gradient)
(1) all active transporters have α-helix domains
i) more flexible than ß-barrel H-bonded structures
(2) Primary active transport
i) couple unfavourable transport against ATP hydrolysis
(a) phosphorylation of enzyme drives conformational change
(3) Secondary active transport
21
(2) Primary active transport
i) couple unfavourable transport against ATP hydrolysis
midterm notes.oo3 (a) phosphorylation of enzyme drives conformational change 05/12/08 11:07:49 AM

(3) Secondary active transport
i) couple unfavourable transport with favourable transport of another substance (down gradient)
ii) act by "rocker switch" mechanism
(a) substrate binding site exposed alternately to cytoplasm and extracellular space in two states
(b) requires that release state has lower substrate binding affinity than first state
b) Passive (along gradient)
(1) facillitated diffusion
(2) ion channel
i) high conduction rates
ii) selectivity
(a) other ions must be excluded
(b) selectivity filter (in K+ channel)
i) geometry of pore matches that of hydrated ion
(A) other ions have different hydration sphere geometries
(B) electrostatic repulsion between the two ions that can occupy selectivity filter prevent tight binding to channel
(c) aquaporins
i) impermeable to protons
ii) pore reorients water molecules to single file
iii) Asn residues at constriction of pore replace H-bonds, preventing proton hopping (Grotthus mechanism)
iii) can be gated
(a) regulated by conformational changes that open and close pore
(b) neuronal Na+ channel is voltage gated
i) opens in response to membrane depolarization
(3) ionophore-mediated
c) simple diffusion
(1) nonpolar
(2) down concentration gradient
(3) eg. CO2
6. ATP synthase
a) reversible

b) converts a proton gradient to ATP if [H+] +
out > [H ]in
c) if [H+] +
out << [H ]in, then synthase acts as proton pump
(1) must be enough to overcome membrane potential drawing protons inwards
d) protons attracted to negative residue in hydrophobic core of rotor, pressed to other side of membrane as rotor turns
7. Intestinal lumen epithelial cells
a) glucose must be pumped from lumen into epithelial cells by Na+-Glc symporter
(1) relatively high Glc concentration in epithelial cells
b) pumped into blood by passive uniporter
X. Nucleotides and Nucleic Acids
A. Nucleotides
1. building blocks of nucleic acids
a) linear polymers form nucleic acids
2. Sugars
a) Ribose
(1) aldopentose with OH groups at every carbon
b) Deoxyribose
(1) ribose with OH missing at C2
3. Nitrogenous bases
a) Purines
(1) 6 chain and 5 chain double bonded rings fused
(2) Adenine

22

i)
a) Purines

midterm notes.oo3 (2) Adenine 05/12/08 11:07:49 AM

i)

(3) Guanine

i)

b) Pyrimidines
(1) single 6 chain doublebonded ring
i) all have at least 1 ketone group
ii) Cytosine
(a) 1 ketone, 1 amino

(b)

iii) Thymine
(a) found in DNA
(b) 2 ketone, 1 methyl

(c)

iv) Uracil
(a) replaces thymine in RNA
(b) thymine without methy group

(c)

c) attached to sugar's C1 by N-ß-glycosyl bond
B. Nucleic Acids
1. successive nucleotides bonded to sugar 3' by phosphodiester bond from phosphate groups on next sugar's 5'
a) new nucleotides always added to 3' end
2. shape
a) DNA exists as a double helix
(1) Theorized by Watson and Crick
(2) proven by Franklin and Wilkins
b) two antiparallel strands complementary to one another
c) stabilized by stacking interactions
3. composition
a) chargaff rule
(1) A+G=T+C
23
3. composition
a) chargaff rule
midterm notes.oo3 05/12/08 11:07:49 AM

(1) A+G=T+C
(2) purines=pyrimidines
b) A H-bonds with T
(1) 2-H bonds
c) G H-bonds with C
(1) 3 H-bonds
4. function
a) sequence of nucleotides encodes amino acid sequences of proteins
5. denaturing
a) when heated, H-bonds break and strands separate
b) when cooled again, helix reforms by annealing
(1) speed depends on whether strands are fully separated
6. melting temperature
a) temperature at which 50% of DNA is denatured
b) depends on ratio of CG to AT
(1) CG has 3 H-bonds; increases melting temperature at higher ratios
7. Mutations
a) caused by chemical modifications of DNA
b) UV exposure
(1) UV radiation causes adjacent thymine bases to bond together into dimers
8. RNA
a) mRNA
(1) copy of DNA sequence that encodes proteins
(2) transfers from chromosome to ribosomes
b) tRNA
(1) match amino acids to mRNA
c) rRNA
(1) structural component of ribosomes
d) enzymatic RNA
(1) process other RNAs
e) Secondary structure
(1) variable
(2) does not form long double helix
i) short complementary sections form hairpins, bulges and loops
(3) non-standard base pairing
i) GU is common

24