Unit 1

Jan 8 - Types of Molecular Interactions

• ionic - interaction of 2 charged atoms based on coulombs law

  

• hydrogen bonds - unequal sharing of a hydrogen atom; a hydrogen atom that is partly shared by 2 electronegative atoms

  • the hydrogen donor is electronegative and tends to pull electrons away from the hydrogen, the result is:

    • hydrogen donor: delta -

      • H is covalently bonded to

    • H: delta +

    • hydrogen acceptor: delta -

      • both are usually O2 or N2, sometimes Suflur

      • is also electronegative and develops a delta -

      • needs a lone pair of electrons

  • how a hydrogen bond is formed: the delta + charged H is attracted to the delta negative acceptor and hydrogen bond is formed

  • H-bonds are weak 4-13 kJ/mole and longer 1.5-2.6 A than covalent bonds

• Van Der Waals Interactions - temporary dipoles; attraction of any 2 molecules

  • at any given time, the charge distribution around an atom is not symmetric

    • result: this asymmetry causes complimentary asymmetric on other atoms, causing them to be attracted to each other

    • has smallest energies of 2-4 kJ/mole

    • attraction inc until the electron clouds start to overlap and repel

      • contact distance is the distance maximal attraction of 2 atoms

• Hydrophobic Interaction - almost all biochemical reactions occur in water

  • water has a big impact on these reactions and interactions

  • structure: has a bent shape, making the molecule polar and capable of forming multiple H-bonds

    • result: water is very cohesive (can form hydrogen bonds with each other); a hydrogen-bonding machine

  • water is an excellent solvent for polar or charged molecules

    • hydrophilic: soluble in water

    • hydrophobic: insoluble in water

    • amphipathic: hydrophilic + hydrophobic groups

  • water can weaken electrostatic interactions by competing for their charge (or partial charge)

    • water reduces electrostatic interactions by 80x (high dielectric constant)

    • result: serious consequences for biological systems, water often needs to be excluded/manipulated to allow various electrostatic reactions to occur

    • water is a double-edged sword: we need it to dissolve, but it interferes with electrostatic interactions

      

Jan 10 - Laws of Thermodynamics

All biological events are governed by a series of physical laws of thermodynamics

I. The total energy of a system (matter in a defines space) and its surroundings is constant; cannot be created or destroyed, can only change form

• ex. burning wood or dropping a ball off a roof

• Enthalpy (H): the heat content of our system

II. The total energy of a system and its surroundings always increases for a spontaneous process

• entropy (S) = randomness

• system or universe increase in entropy for a reaction to go forward

• ex. goes from ordered system to a more disordered one

• Things can become more ordered

  • entropy can be decreased locally in the formation of ordered structures ONLY if the entropy of the universe is increased by an equal or greater amount

  • entropy decreases in system (2 molecules going to 1 molecule) but heat is released causing the entropy around the system (ex. the universe) to increase

    • TLDR: reaction releases heat, causing entropy of the universe to increase, which is greater than the decrease of entropy in the system

  • we can exist only if we make the universe more disordered

• How to Measure Spontaneity

  • ΔG = ΔHsys - TΔSsys

    • T = temp in K

    • ΔG is gibbs free energy measured in KJ/mole

  • Spontaneity = how likely a reaction or process will occur

    • doesn’t define how fast a reaction is, only if the reaction will occur

      • ΔG < 0 = the reaction is spontaneous

      • ΔG > 0 + the reaction is non-spontaneous

        Enthalpy/Entropy	Affect on ΔG
        ΔH < 0 (ex. releasing heat)	ΔG becomes more negative and the reaction becomes more spontaneous
        ΔS > 0 (ex. reaction becomes more disordered)	ΔG becomes more negative and the reaction becomes more spontaneous

• Why you want to know ΔG → reactions needs to be spontaneous to occur in the cell (ΔG = no reaction)

Jan 10 - Entropy & The Hydrophobic Effect

• Hydrophobic molecules cluster together since the entropy is more favorable

  • hydrophobic molecule entropy decreases

  • water entropy increases - more hydrogen bonds with water, more ordered

• Fig 2-7b page 48: when a non-polar molecule is added to water, the water molecules are forced into a cage around the hydrophobic molecule

  • result: lowers entropy since water is becoming ordered

• when 2 non-polar molecules come together, fewer water molecules are needed to form the cage around the non-polar molecules

  • result: entropy increases; favors non-polar molecules to cluster together (not a direct force pulling the 2 molecules together)

Jan 10 - Ph and Buffers

The concentration of hydrogen ions within biological systems is critical

• Why? Most biomolecules (not all) act as weak acids or bases (ex. their functional groups can be ionized)

• Figure 2-6: amino acid and nucleotide charge changes with plot

  • changing pH may change the way a molecule behaves since it can affect its ionization state

  • molecule behavior depends on ionization state

• [H] is measured as pH

  • pH = -log[H]

  • scale of 0-14

    • 0 = strongly acidic

    • 14 = strongly basic

• How do we maintain a pH of a cell (7.2-7.4)? Weak acids can act as buffer

  • weak acid = an acid that is not completely ionized in solution

    • acid - gives up protons

    • base - proton acceptor

  • HA ←→ A^- + H^+

  • pKA = -logKa

    

• we can calculate the pH of any solution of a weak acid if we know the molar ratio of a conjugate base to acid and pKa → Henderson Hasselbalch Equation

  • pH = pKa + log[A]/[HA]

  • if we titrate a weak acid (ex. acetic acid) with a strong base (NaOH) we can see the following:

    • pH = pKA → [HA] = [A]

    • pH < pKa → [HA] > [A] → more acid than conjugate base

    • pH > pKa → [HA] < [A] → conjugate base is more dominant form

• Fig 2-16: there is a region where the pH doesn’t change very much even though a large amount of acid (or base) are being added

• buffering region: a mixture of a weak acid and a conjugate base in a 1:1 ratio

  • function: resists changes in pH because both forms are present and can either soak up or release a proton

  • pH = pKa here

  • the buffering region is usually +/- pH unit from pKa unit

    • ex. if pKa is 4.76, pH is 3.76

  • buffers fail when there is only the acid or conjugate base present

  • you want the buffer to have a pKa = 7

• Fig 2-18: buffer gives away proton, turning into the conjugate base (acetate)

  • if HCI is added, the pH will drop (increasing [H])

  • pH will go down slowly if you add both acetic acid and acetate since acetate will soak up the proton, turning it into acetic acid

• Types of Buffers

  1. Bicarbonate (more complicated)

     • CO2 (dissolved) + H2O ←→ H2CO3 (carbonic acid) ←→ H + HCO3 (bicarbonate)

     • approximate pKa of 6.1, would buffer from 5-7

  2. Phosphate

     • H2PO4^- ←→ H + HPO4^-2

     • pKa of 7.1, buffering rage 6.2 - 8.2

  3. Histidine and Cysteine

     • amino acids

     • Histidine pKa = 6; Cysteine pKa = 8

Jan 13 - Protein and Amino Acid Structure

• protein: linear polymer built of amino acids

  • structure: final shape depends on its sequence of a.a

  • a.a contain a variety of functional groups, allowing for massive diversity

  • proteins can interact with each other or molecules to form complexes

  • proteins can be flexible or rigid

• amino acid: the “ultimate lego set”

  • Structure:

    1. alpha carbon

    2. carboxylic acid/ carboxyl group (COOH/COO-)

       • the form that exists depends on pH

       • the carbon is chiral: an atom that has 4 different functional groups; not superimposable on its mirror image

         • thus there are 2 enantiomers of each amino acid, except for glycine (R group is hydrogen)

         • enantiomer: a pair of molecules each with one or more chiral center that are mirror images of each other

    3. hydrogen

    4. unique R side-chain

       

• FIG 3-2: amino refers to NH3 group, acid refers to carboxyl group - all attached to an alpha carbon

• Determining L or D

• carboxyl group is above central carbon, and R group is below

  • L amino acid = if amino group (NH3) is on left to alpha carbon

  • D amino acid = if amino group (NH3) is on right to alpha carbon

• In biological systems only the L-amino acids exist (with very few exceptions) in proteins and living systems

  • furthermore almost all L-amino acids are in the S-configuration

    

• Ionization of amino acids

• all amino acids have 2 ionizing group (carboxyl and amino group), often 3 (R-group)

  • carboxyl pKa = 2

    • pH 0-2 - COOH dominates

    • pH 2 - 14 - COO- dominates

  • amino group pKa = 9

    • 0 - 9 - NH3+ dominates

  • Hence, at pH 7 amino acids exist as zwitterions: ions with both positive and negative charges

• Types of Amino Acids

  • basic and acidic amino acids are often found on the surface of proteins (interact with water and away from the hydrophobic amino acids)

  • you can vary the amino acid by changing the side-chain (R-side chain)

    • there are 20 key amino acids and these (or slight modifications are used in all living things

    • you have to know all 20 amino acids (draw them), their structures, names, and abbreviations

Jan 15 - I. Nonpolar, Aliphatic R groups

Non-polar, aliphatic: all are hydrophobic and will tend to cluster together

• different sized and shaped R-groups allow for close packing

• usually found in the center of a protein, away from the water

• usually not reactive

• aliphatic: compounds with an open chain structure (alkane)

II. Aromatic R-groups

Aromatic Amino Acids: contain aromatic rings (ex. phenyl rings)

• participate in hydrophobic interactions

• usually found in the core of proteins

III. Basic Amino Acids - Positively Charged R Groups

Basic Amino Acids (positively charged, high pKas)

• lysine and arginine are both positively charged at pH 7 (pKas > 10)

• Mea culpa: my grievous fault; the imidazole of His is aromatic, but we don’t classify it as aromatic

Jan 17 - IV. Acidic Amino Acids - Negatively Charged

Acidic Amino Acids - negatively charged

• contain carboxyl groups as R groups

• negatively charged at pH 7 (pKas < 4)

V. Polar, Uncharged R groups

• not charged at pH 7

• can H-bond, more hydrophilic

• note: the pKa for an R group of an amino acid can change depending on the environment (see page 2 of problem set 2)

• dont have to remember pKa, just now the conjugate base and acid form

Protein Structure

Jan 20 - I. Primary Structure

I. Primary Structure (1 degree) - linear sequence of amino acids linked by peptide bonds to form a polypeptide

• peptide bond - linkage of alpha-carboxyl linked to the other alpha-amino group of another amino acid with the loss of water

  • not energetically favorable, but once formed stable

    • delta G to break the peptide bond is more favorable (rather be single amino acids) - the activation energy to break a peptide bond is very high

• polypeptide - a series of amino acid residues linked by peptide bond

  • structure

    • have polarity

      • not referring to charge, the ends are different (the end that has a free amino - NH3 group)

      • free amino group should always be on left, free carboxyl group is on right

    • residue - an amino acid unit in a polypeptide

    • contain a backbone which repeats (NCC)(NCC) with variable side chains

      • the backbone is hydrophilic

      • carbonyl and amino group can H-bond, except proline which has limited H-bonding ability

  • molecular weights of proteins are expressed in Daltons or more commonly Kilodaltons (kDa)

    • 1 Da = mass of hydrogen atom = 1g/mole

  • each protein has a unique primary amino acid sequence

  • primary sequence is encoded in the DNA

  • knowing the primary amino acid sequence allows us to determine the

    1. determine shape - 3D shape of a protein depends on primary sequence

    2. determine function

    3. understand disease

    4. understand evolutionary history

• polypeptides are flexible but conformationally restrained

  • what does this mean? the peptide bond has double bond characteristics due to resonance between the peptide bond and the carbonyl

    • result:

      1. the peptide bond is planar. This in turn locks a series of atoms into a plane

      2. no rotation about the peptide bond

      • since peptide bond acts like a double bond, the peptide bond could be in cis or trans orientation

        • cis = same direction

        • trans = pointing in diff directions

        • due to steric hindrance, all peptide bonds are in trans (except for x-pro peptide bond where both cis and trans occur)

        

• fig 4-2: are all in one plane; can’t rotate around the peptide bond

• this partly explains the conformationally restrained part, but what about flexibility?

• the bond between N-Calpha and C=O-C-alpha are free to rotate

  • result: provides flexibility, allowing the backbone to fold in many ways

  • we measure the amount of rotation about the bond as the dihedral angle (torsion angle)

    • ranges from - 180 to + 180

  • N - Calpha dihedral angle = phi = φ

  • C=O-C-alpha dihedral angle = psi = Ψ

• not all combinations of phi and si are allowed due to steric hinderance, limiting the number of structures a protein can adopt

  • the combination of phi and si that are possible are shown in a Ramachandran plot

    

    • ex. lysine, has H as an R-group, less clashing so more blue

    • ex. proline, has an R-group ring and covalently bonded to nitrogen - phi are the ones restrained since ring will block it from doing so

• Ramachandran plot

  • darker shade = very favorable

  • lighter shade = less favorable, but possible

  • white shade = not permitted

  • most amino acids have similar plots to L-Ala

    • note: ¾ of all dihedral angles are not permitted

• bringing this all together

  • large molecules that can freely rotate among many bonds will assume random coils (no defined final structure; a mix of different structures)

  • because proteins have a series of limitations on what orientation they adopt

    • 1st limitation: double bond characteristic, planar peptide bonds

    • 2cnd limitation: the dihedral angles, phi and si

  • thus, they can often spontaneously fold into a single structure

• FIG 3-14: should be written as H3N - S - G - Y - A - L - Coo^-

Point Mutations

• K 614 P

  • K = original amino acid

  • 614 = location in primary sequence from the N terminal end

  • P = new amino acid

• ex. describe E6V mutation in the beta-glonin protein

  • E = glutamine - acid/negatively charged charge

  • V = valine - r-group is non-polar aliphatic

  • went from negatively charged to a hydrophobic group

  • each hemoglobin protein consists of 2 alpha-globin and 2 beta-globin subunits

  • creates a new hydrophobic patch on the surface of T-state hemoglobin and allows to self-polymerize

    • rods are inflexible, causing sickle cell anemia

    • sickle cells go through capillary beds, doesn’t twist and flex and hurts our capillaries (don’t need to know, just know the effect of a singe point mutation)

Jan 22 - II. Secondary Structure - Alpha Helix

II. Secondary Structure - spatial arrangement for amino acid residues in a polypeptide that are relatively close to each other in linear sequence

• alpha helices and beta strands/sheets - the common types of secondary structures

  • alpha helix - a polypeptide backbone forms the inner part of a right handed helix, with the side chains sticking outwards

    • structure

      • the helix is stabilized by intrachain hydrogen bonds between the NH and C=O groups of the backbone

        • intrachain = hydrogen bonds are within the backbone

      • R-groups are almost perpendicular to the axis of the helix

      • has ideal dihedral angles of phi - 60 and psi -45

      • the C=O of residue i forms an H-bond with the N-H or residue i + 4 (ex. 4 residues further towards C-terminus) - see diagram below

        

      • the helix is almost always right handed

        • left handed and right handed alpha helix are not the same (not superimposable)

          

      • all the NH and C=O in the backbone are H-bonded, except the ends

      • each amino acid residue in the helix increases the helix length by 1.5 angstroms

        • helix rises by 1.5/# of amino acids

      • r-groups of i, i +1 and i+2 point in different directions

      • r-groups of i, i +3 and i + 4 point in similar directions

        • important because it aids in an ampithatic molecule

      • left handed helices are permitted but rare (not as stable)

      • alpha helices are show as twisted ribbons or rods

        

    • alpha helical content of a protein can vary

      • some proteins have no alpha helices

      • some proteins are just alpha helices

      • usually alpha helices are less than 45 angstroms

      • 2 alpha helices can intertwine into coiled coils (ex. our hair)

        

    • alpha helices are a series of planes that are coiling due to double bond characteristics of peptide bonds

      

  • beta-pleated sheets - two or more beta-strands (usually a polypeptide strands from the same molecule) associated as stacks on chains in an extended zigzag form

    • stabilized by interstrand hydrogen bonds

    • beta strands are the components that make up a beta sheet

    • has little zigzags or pleats (each pleat is the plane of a peptide bond)

      

  • for an antiparallel beta-sheet

    • each amino acid extends the beta strand by 3.5 A (more spread out than an alpha-helix)

    • r-groups are adjacent of adjacent residues point in opposite directions perpendicular to the plane of the strand or sheet

    • the strands are organized into beta-sheets

    • strands run in opposite directions, the N-H and C=O of a single residue i on one beta-strand h-bonds to the single residue j on the other beta-stran opposite to it

    • has ideal dihedral angles of phi - 139 and psi + 135

      

  • B-sheets can also be parallel. It’s like an antiparallel B-sheet, except:

    • instead of doing straight down H-bond, it does 2 reaches (shortens length of beta strand + causes dihedral angle to be twisted)

      • each residue in the beta strand only extends the B-strand by 3.25 A

      • has ideal dihedral angles of -119 phi and +113 psi

      • the N-H of residue i on one B-strand H-bonds to residues j C=O in the other strand

        • C=O of residue in i in the first strand H-bonds to j + 2 N-H in the second strand

  • Mixed B-sheets (both parallel and antiparallel)

    • B-strands are depicted as broad arrows pointing towards the C-terminal end

    • the distance between B-strands in primary amino acid sequence can be small or large

    • beta-strands can be short or long

    • beta-sheets can be flat or twisted

    • it can even twist back on itself to form a beta-barrel

      

when drawing out a polypeptide backbone, draw the backbone as a zigzag

• forces us to draw it as trans

  

III. Tertiary Structure

Tertiary Structure - the spatial arrangement of amino acid residues that are far apart from each other in linear sequence as well as the pattern of disulfide bonds

• BIG MONEY = the 3D structure

• each protein tertiary structure is different

• tertiary structure is limited to a single polypeptide that folded into a structure

  • ex. myoglobin

    • O2 storage protein in mammalian muscles

    • single polypeptide chain of 153 amino acids

    • contains a heme group (iron in a protophyrin ring) where the O2 binds to

    • 70% of the chain is in alpha helices (8 helices)

      • most of the rest are in loops and turns

    • the core of the protein is almost exclusively composed of hydrophobic residues (except for a his which is needed by the heme)

    • the surface is composed of more polar/charged residues (and some non-polar)

  • quick note about myoglobin: binds O2 with high affinity and only releases if when [O2] is really low

• why would you wanna know the structure of myoglobin? structure helps us understand function

  • helps us identify possible places for drug binding

• some proteins have multiple compact structures called structural domains linked by flexible sections of the polypeptide (often with no defined structure)

  • no defined structure = structure is moving around

    

• in most tertiary structures, the dihedral angles for each residues fall into permissible areas of a Ramachandran plot

  

jan 27 lecture

IV. Quaternary Structure

Quaternary structure: the spatial arrangement of multiple folded subunits (folded polypeptides) and the nature of their interactions along with the disulfide bonds between subunits

• some proteins are composed of more than one folded polypeptide chains (subunits)

  • homomers - the subunits can be identical

  • heteromers - when the subunits are different

• some proteins must be multimers in order to function

• protomer - the base unit in a quaternary structure

  • usually repetitive

  • usually (not always) monomeric in nature but the structure is not the same as the monomer

    • protomer is what it looks like in the final structure

  • fig 2-22 pg 128

• ex. hemoglobin

  • the O2 transporter in mammals

  • composed of 4 subunits

    • 2 alpha subunits (alpha-globins)

    • 2 beta subunits (beta-globins)

  • will cover in much more detail later, but it is the interactions between the subunits that are critical for function

    • hemoglobin cannot function unless it is a tetramer

  • the protomer for hemoglobin is an alpha-beta dimer

• ex. minute virus of mice

  • 9 UPI 2 subunits of 51 UP2 subunits to form an isohedral capsid with just enough room to fit the viral DNA

Protein Folding

• even with limitations on the backbone, there are trillions of possible structures a polypeptide could adopt and it would take forever for a protein to try every single structure

  • however, most proteins spontaneously fold into just one structure in seconds

• up until a few years ago, we couldn’t predict a protein’s tertiary structure based off of primary sequence, but now AI programs such as Alphafold2 or rosettafold can!

• we do know that folding is driven by thermodynamics

  • ex. finding the most stable complex (most negative delta G)

  • note: the difference in free energy between folded and unfolded is small (20-60 kJ per mole)

  • this is mostly (but not all) driven by entropy (ex. the hydrophobic residues are excluded from water in the core, while hydrophillic residues are on the surface)

    • backbone of a polypeptide is polar, when it folds, some parts of the backbone is in the core (not favorable).

  • in order to bury the polar backbone of a polypeptide in the core, it needs to H-bond

    • many alpha-helices and beta-sheets are amphipathic (one side is hydrophobic, the other is hydrophilic)

  • unpaired charged or polar group in the hydrophobic core tend to destabilize the structure

• Q: can a portion of a primary sequence define a secondary structure?

  • A: yes and no

  • certain amino acid residues are more likely or less likely to be found in a stabilized (or destabilized) alpha-helices and beta-strands/sheets

  • table 4-2 - proline and glycine are alpha-helix wreckers, and to a lesser extend beta strand wreckers

    • proline has the ring, dihedral angle is limited and can’t twist into the optimal angle for an alpha helix

    • proline has limited h-bond capabilities since it doesn’t have N-H in its backbone (has N-R instead)

    • glycine has a hydrogen in its r-group

  • however, experiments have shown that the exact same portion of sequence in 2 different proteins can adopt 2 different secondary structures

    • thus we cant always determine the secondary structure by looking at a portion of primary sequence

    • the overall teritiary structure influences secondary structure

  • what else do we know?

    1. folding tends to be an all or non process

       • usually you’re folded or you’re not

    2. it is cooperative

       • ie. as one portion of the protein folds (ex. beta sheet) it will influence how another portion folds

         • thus, we don’t have to sample every structure FIG 4-26 pg 131

       • however, there is usually many possible pathways, so we often depict folding as a free-energy funnel FIG 2-27 pg 132

       • in a proteins unfolded state, there are many possible structures with high free energy, but as those species fold the free energy decreases until you reach the folded state

       • the farther you go into folding, there are more limitations to the types of structures you can get\

       • there are multiple folding routes to get you to the final structure

jan 29

• not all proteins have a single 3D structure

• some proteins only fold into a single structure when they bind something

• some proteins are in equilibrium between 2 structures

• determining structure of intact proteins (big deal)

  1. x-ray crystallography

     • use x-ray to measure e- density

     • how the structure of myoglobin; hemoglobin were determined

  2. nuclear magnetic resonance (NMR)

     • measures the location of nuclei

  3. cryo-electron microscopy

     • uses a beam of e- to visualize a frozen protein

• post-translational modifications (after protein synthesis)

  1. phosphorylation - attachment of phosphate group, usually to the OH of an R-group

     • commonly phosphorylated residues: Ser, Thr, Tyr

     • activates or inactivates a protein by adding a negative charge

  2. glycosylation - attachment of a sugar or carbohydrate to an amino acid residue (usually, Asn, Thr, Ser)

     • surface labelling

     • most proteins on the cell surface are glycosylated

  3. hydroxylation - adds an OH (usually proline)

     • result: becomes more polar

     • fibre stabilization

  4. carboxylation - adds a carboxyl group (usually to glu)

     • important in clotting

  5. acetylation - addition of an acetyl group to an NH3 (amino) - (ex. lysine)

     • (insert pic of the acetyl group)

• most proteins are cleaved or trimmed after synthesis

  • this could activate or inactivate them

    • ex. fibrinogen → cut → fibrin (forms clot)

    • multiple proteins can be formed from a single long polypeptide

      • result: multiple mature protein

      • ex. viruses like to do this

Enzyme Thermodynamics & Kinetics

• enzyme - biological macromolecule (usually protein) that acts as a catalyst for biochemical reactions

  • “work horses of the cell”

• catalyst - chemical that increases the rate of a reaction without being consumed

  • Thus, enzymes speed up reactions

• enzymes are very specific, they will only catalyze on specific set of reactions

  • papein: enzymes that cleaves peptide bonds in a polypeptide

  • trypsin: only cleaves peptide bonds on the carboxyl side of lys and arg

  • thrombin: only cleaves peptide bonds only between and arginine and glycine

• specificity is based on a series of weak interactions between the substrate and the enzyme, specifically in the active site

• dont want too many interactions

  • the shape of the enzyme determines specificity and function

  • active site: region of the enzyme that binds the substrate

    • it contains the residues that directly participate in the reaction

    • characteristics of active site:

      • they are clefts (aka dimples) in the enzyme made up of residues from all over the primary sequence

      • take up a small volume of the enzyme

      • water is usually excluded or manipulated from the active site

      • the substrate is bound to the active site by a series of weak interactions

• thus, the substrate and the enzyme must be partly complimentary, otherwise the substrate can’t bind and catalysis cannot occur

• can occur by

  1. lock and key

  • active site is a complimentary match to the substrate (rare)

  • 2. induced fit

  • binding of the substrate causes the active site to assume a matching shape

jan 31

• the hyperbolic curve = equilibrium

1. enzymes do not alter the final equilibrium of products to reactants (see slide)

2. enzymes do not alter delta G of reaction, they obey the laws of thermodynamic

   • ex. they can’t change the spontaneity of a reaction if delta g reaction is positive, it is non-spontaneous and adding enzymes will not change that (fig 1-29 pg 26)

3. enzymes do speed up the rate of a reaction

   • how do enzymes do this?

     • enzymes accelerate reactions by decreasing the activation energy (delta g double dagger) by facilitating the formation of the transition state (X double dagger)

     • imagine a substrate being converted to product (S → P)

     • in order to form products, the substrate goes through a transition state (x double dagger), the transition state has the highest G in the reaction and the lowest concentration

     • the energy needed to get x double dagger is known as the activation energy (delta g double dagger)

     • usually the activation energy (g double dagger S → P =) (insert picture of formula

       • activation energy from S → P

       • activation energy P → S

     • the activation energy controls the reaction rate

       • only a fraction of S will have enough energy to form the transition state (x double dagger)

       • note: the activation energy is not part of the overall delta g of reaction calculations because the energy put in is returned when the transition state is converted to products

     • fig 6-3 page 181

       • for S+ E ←→ES ←→ EP←→ E + P

       • enzymes interact with the transition state such that the activation energy is lowered

         • therefore, the reaction speeds up as as greater fraction of S has the energy to reach the transition state (X double dagger)

         • where does the energy come from to lower the activation energy?

           • comes from the enzyme binding and stabilizing the transition state (x double dagger)

           • the active site of an enzyme is perfectly complimentary to the transition state (x double dagger)

           • we call the energy stabilizing the transition state in an enzyme the binding energy (delta Gb)

           • delta Gb = delta delta G (change in activation energy) = delta g ++ - delta g ++ catalyzed

           • the energy is derived from the non-covalent interactions between the enzyme and the transition state

END OF MATERIAL FOR MIDTERM