Biochem ch 2-6

water, Proteins, 3D Proteins, Protein fucntions, Enzymes Catalysis

Ionic (Coulombic) Interactions

Electrostatic interactions between permanently charged species,

or between the ion and a permanent dipole

Dipole Interactions

Electrostatic interactions between uncharged, but polar molecules

Van der Waals Interactions

Weak interactions between all atoms, regardless of polarity

– Attractive (dispersion) and repulsive (steric) component

Hydrophobic Effect

Complex phenomenon associated with the ordering of water molecules around

non-polar substances

Noncovalent Forces and Interactions

Hydrogen bonds

• Ion-Ion 1/r

• Ion-dipole 1/r2

• Dipole-dipole 1/r3

• Dipole - Induced

dipole - 1/r5

• ID – ID (Van der

Waals) - 1/r6

• Hydrophobic

Hydrogen Bonds

Strong dipole-dipole or charge-dipole interaction that arises

between an acid (proton donor) and a base (proton acceptor)

• Typically involves two electronegative atoms (frequently

nitrogen and oxygen)

• Hydrogen bonds are strongest when

the bonded molecules are oriented to

maximize electrostatic interaction.

Van der Waals Interactions components

two components:

– Attractive force (London

dispersion) Depends on

the polarizability

– Repulsive force (Steric

repulsion) Depends on

the size of atoms

Van der Waals Interactions significance

Weak individually

–Easily broken, reversible

• Universal:

–Occur between any two atoms that are near each other

• Importance

– determines steric complementarity

– stabilizes biological macromolecules (stacking in DNA)

– facilitates binding of polarizable ligand

Water solvent interaction

Good- charged and polar such as amino, peptides, smal alcohol, carbohydrates

Poor- nonpolar such as nonpolar gases, aromatic, aliphatic chains

Water interaction to salts

high dielectric constant shields oppositely charged ions. Entropy increases as orded crystals lattice is dissolved

Ice

hexagonal ice forms regular lattice, low entrophy

Hydryphobic effect

association or folding of non-polar molecules aq. solutions, DOES NOT arise because of some attractice direct force between two non-polar molecules

hydrophobic main factors behind:

protein folding, protein-protein association, formation of lipids micelles, beding of steroid hormones to their receptors

Reasons low solubility hydrophobic solute

disruption of H-bonded H2O network, cavity formation in a medium with high surface tension Lipid molecules disperse in the

solution; nonpolar tail of each lipid

molecule is surrounded by ordered

water molecules

• Lipid aggregates – Water released,

surface area reduced

Colligative Properties

boiling point, melting point, and osmolarity

Effect of Extracellular Osmolarity

isotonic, hypertonic and hypotonic

Proton Hydration

immediately hydrated to form hydronium (oxonium) ions, associated with one of the non-bonding electron pairs

Ionization of Water:

Quantitative Treatmen

Concentrations of participating species in an equilibrium process

are not independent but are related via the equilibrium constan

pH formula

pH=-log[H+]

pKa measures?

acidity, string acids → larger Ka→ small pKa

Buffers

mixture weak acids + anions, resist change of pH, Buffering capacity of acid/anion system is greatest at pH = pKa

Henderson–Hasselbalch Equation

3 elements primarly involve in hydrogen bonding

Hydrogen, Oxygen, Nitrogen

examples weak acids, balanced chem reaction with water, describe how different than strong acid

CH3COOH+H20 →H3O+CH3COO

Weak acids only partially ionize in water, meaning the majority of the molecules remain un-dissociated. Strong acids CH3COOH or HCl ionize completely into their ions in aqueous solution. a weak acid solution has a higher $\text{pH}$ (less acidic) and reacts more slowly with bases or metals compared to a strong acid because of the lower concentration of free H3O ions.

Amino Acids

Building blocks, protein are heteropolymers of alpha aminos, chiral

Amino acids fucntions

Capacity to polymerize

– Useful acid-base properties

– Varied physical properties

– Varied chemical functionality

Aliphatic aminos

Hydrophobc side chain

Alanine/Ala/A

Valine/Val/V

Isoleucine/Ile/I

Leucine/Leu/L

Methionine/Met/M

Aromatics aminos

Ring

Phenylalanine/Phe/F

Tyrosine/Tyr/Y

Tryptophan/Trp/W

Charged aminos

electricaly charged side chain, positive: Arg,His,Lys. Negative: Asp, Glu

Arginine/Arg/R

Histidine/His/H

Lysine/Lys/K

Aspartic acid/Asp/D

Glutamic acid/Glu/E

Polar aminos

polar uncharged side chain

Serine/Ser/S

Threonine/Thr/T

Asparagine/Asn/N

Glutamine/Gln/Q

Special aminos

Glycine, Proline, Cysteine, Selenocysteine

Glycine/Gly/G

Proline/Pro/P

Cysteine/Cys/C

Selenocysteine/Sec/U

Ionization of aminos

At acidic pH, the carboxylgroup is protonated and the amino acid is in the cationic form

At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The netcharge is zero; such ions are called Zwitterions

At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic form

aminos charge 0

amino acid without ionizable side chains, the Isoelectric

Point (equivalence point, pI), the net charge is zero

Structure of Proteins

This structure is able to fulfill a specific biological

function

• This structure is called the native fold

• The native fold has a large number of favorable

interactions within the protein

• There is a cost in conformational entropy of folding

the protein into one specific native fold

Favorable Interactions in Proteins

Hydrophobic effect

– Release of water molecules from the structured solvation layer

around the molecule as protein folds increases the net entropy

• Hydrogen bonds

– Interaction of N-H and C=O of the peptide bond leads to local

regular structures such as -helixes and -sheets

• London dispersion

– Medium-range weak attraction between all atoms contributes

significantly to the stability in the interior of the protein

• Electrostatic interactions

– Long-range strong interactions between permanently charged

groups

– Salt-bridges, esp. buried in the hydrophobic environment strongly

stabilize the protein

Structure of the Peptide Bond

The resonance causes the peptide bonds

– be less reactive compared to e.g. esters

– be quite rigid and nearly planarRotation around bonds connected to the alpha

carbon is permitted

• (phi): angle around the alpha-carbon—amide

nitrogen bond

•(psi): angle around the beta-carbon—carbonyl

carbon bond

Ramachandran plot significance

Ramachandran plot shows the distribution of psi and phi

dihedral angles that are found in a protein

• shows the common secondary structure elements

• reveals regions with unusual backbone structure

Secondary Structures

alpha helix: h-bonds between nearby residues

beta sheets: h-bondds between adjacent segments not nearby

Random coil: Irregular arrangement of the polypeptide chain

alpha helix

Helical backbone is held

together by hydrogen bonds

between the nearby

backbone amides

• Right-handed helix with 3.6

residues (5.4 Å) per turn

• Peptide bonds are aligned

roughly parallel with the

helical axis

• Side chains point out and

are roughly perpendicular

with the helical axis

interactions of aminos + alpha helix

Not all polypeptide

sequences adopt alpha-helical

structures

• Small hydrophobic residues

such as Ala and Leu are

strong helix formers

• Pro acts as a helix breaker

because the rotation around

the N-Ca bond is impossible

• Gly acts as a helix breaker

because the tiny R-group

supports other

conformation

Helix Macro-Dipol

Peptide bond has a strong

dipole moment

– Carbonyl O negative

– Amide H positive

• All peptide bonds in the 

helix have a similar

orientation

• The  helix has a large

macroscopic dipole

moment

• Negatively charged

residues often occur near the positive end of the

helix dipole

beta sheets

The planarity of the peptide

bond and tetrahedral geometry

of the alpha-carbon create a

pleated sheet-like structure

• Sheet-like arrangement of

backbone is held together by

hydrogen bonds between the

more distal backbone amides

• Side chains protrude from the

sheet alternating in up and

down direction

parallel b-sheets

H-bonded strands run

in the same direction

antiparallel b-sheets

H-bonded strands

run in opposite directions

Beta turns (hairpins)

change the direction

• The 180° turn is accomplished over four amino acids

• The turn is stabilized by a hydrogen bond from a carbonyl oxygen

to amide proton three residues down the sequence

• Proline in position 2 or glycine in position 3 are common in beta-turns

Proline isomers

For peptide bonds involving proline, about 6-20%

can be in the cis configuration

• Proline isomerization is catalyzed by proline

isomerases

Protein Tertiary Structure

fibrous proteins

globular proteins

Fibrous proteins

typically insoluble; made from a single secondary structure

strcture to function

alpha-keratin, collagen

globular proteins

water-soluble globular proteins

lipid-soluble membraneous proteins

Quaternary structure

ormed by spontaneous

assembly of individual polypeptides into a larger

functional cluster

Chaperones

prevent misfolding, facilitate,

function of globular protein

Storage of ions and molecules

– myoglobin, ferritin

• Transport of ions and

molecules

– hemoglobin, serotonin

transporter

• Defense against pathogens

– antibodies, cytokines

• Muscle contraction

– actin, myosin

• Biological catalysis

– chymotrypsin, lysozyme

ligand

molecule that binds at binding site via non-covalent forces, which

enables the interactions to be transient

Binding: Quantitative Description

association rate constant ka

the dissociation rate constant kd

After some time, the process will reach the

equilibrium where the association and

dissociation rates are equal

• The equilibrium composition is characterized

by the the equilibrium constant Ka

Analysis in Terms of the

Bound Fraction

fraction of occupied binding sites, In terms of the more commonly used

equilibrium dissociation constant

Specificity: Lock-and-Key Model

Proteins typically have high specificity: only certain ligands bind

• High specificity can be explained by the complementary of the

binding site and the ligand.

•Complementarity in

– size,

– shape,

– charge,

– or hydrophobic / hydrophilic character

•“Lock and Key” model by Emil Fisher (1894) assumes that

complementary surfaces are preformed

Specificity: Induced Fit

Conformational changes may occur upon ligand binding

(Daniel Koshland in 1958).

– This adaptation is called the induced fit.

– Induced fit allows for tighter binding of the ligand

– Induced fit can increase the affinity of the protein for a

second ligand

• Both the ligand and the protein can change their

conformations

function myoglobin

Need to store oxygen for metabolism

• Protein side-chains lack affinity for O2

• Some transition metals bind O2 well but would generate

free radicals if free in solution

• Organometallic compounds such as heme are more

suitable but Fe2+ in free heme could be oxidized to Fe3+

if two heme molecules share an oxygen molecule

• Solution:

– Capture the oxygen molecule with heme that is

sequestered inside the protein

– In mammals, myoglobin is the main oxygen storage

protein

Structures of Porphyrin and Heme

Binding of Carbon Monoxide

CO has similar size and shape to O2; it can fit to the same

binding site

• CO binds over 20,000 times better than O2 because the

carbon in CO has a filled lone electron pair that can be

donated to vacant d-orbitals on the Fe2+

• Protein pocket decreases affinity for CO, but is still binds

about 250 times better than oxygen

• CO is highly toxic as it competes with oxygen. It blocks the

function of myoglobin, hemoglobin, and mitochondrial

cytochromes that are involved in oxidative phosphorylation

How Can Affinity to Oxygen Change

Like This?

Must be a protein with multiple binding sites

• Binding sites must be able to interact with each other

• This phenomenon is called cooperativity

– positive cooperativity: first binding event

increases affinity at remaining sites

– negative cooperativity: first binding event

reduces affinity at remaining sites

Positive cooperativity can be

recognized by sigmoidal binding

curves

Hill equation

What is the term that scientists use to compare the binding affinity of ligands? Give 2 (non-numerical) examples of a ligand binding to a protein.

The term scientist use to compare the binding affinity of ligads is the dissociation constant K_d. 

1) oxygen binding to hemoglobin 

2) enzyme binding

Myoglobin contains the _____________ prosthetic group and the ________ ion that allow for reversible to _____________ and nonreversible binding to _________________. 

Myoglobin contains the heme prothetic group and the iron ion that allows for reversible to Oxygen and nonreversible binding to Carbon Monoxide 

Hemoglobin contains 2 _______ subunits and 2 ________ subunits and exists in either the ___________state or the _______ state.  

Briefly describe the O₂ binding cooperativity in Hemoglobin.

Hemoglobin contains 2 alpha helixes subunit and 2 beta subunits and exist in either the Tense state or Relaxed state 

alpha, beta, T(tense), R(relaxed) Increase the affinity of remaining subunits for oxygen. Goes from a T state to R state meaning easier binding

The image below is a typical structure of an immunoglobulin G (IgG), identifying the 2 heavy chains, 2 light chains, and which region is most variable. 

Light chain: A/B left, G/H right, Heavy chains: C,D, F, E, Most variable: A and H 

Enzyme?

Enzymes are catalytically active biological

macromolecules

• Specific, Efficient, Active in Aqueous Solution

• Most enzymes are globular proteins,

however some RNA (ribozymes, and ribosomal RNA) also

catalyze reactions

Non-peptide Co-Factors (Metals, Vitamins, Coenzymes)

• Enzymes can be classified functionally

Biocatalysis?

Higher reaction rates

• Greater reaction specificity

• Milder reaction conditions

• Capacity for regulation

Metabolites have

many potential

pathways of

decomposition

• Enzymes make the

desired one most

favorable

enzymatic Substrate Selectivity

Kinetics and Equilibrium

Enzymes affect rates but not equilibria

Transition State Theory

Slow reactions face significant activation

barriers that must be surmounted during the

reaction

–transition state theory is applicable for

catalysis

–rate constants and free energies can be

related

Rate Acceleration

The enzyme

lowers the

activation barrier

compared to the

uncatalyzed

aqueous reaction

How to Lower changeG‡?

Enzymes organizes reactive

groups into proximity

• Uncatalyzed bimolecular reactions:

two free reactants  single restricted transition state

conversion is entropically unfavorable

• Uncatalyzed unimolecular reactions:

flexible reactant  rigid transition state conversion is

entropically unfavorable for flexible reactants

• Catalyzed reactions:

Enzyme uses the binding energy of substrates to organize

the reactants to a fairly rigid ES complex

Entropy cost is paid during binding

Rigid reactant complex  transition state conversion is entropically OK

How is TS Stabilization Achieved?

acid-base catalysis: give and take protons

– covalent catalysis: change reaction paths

– metal ion catalysis: use redox cofactors, pKa shifters

– electrostatic catalysis: preferential interactions with TS

acid-base catalysis

give and take protons,

metal ion catalysis

use redox cofactors, pKa shifters

electrostatic catalysis

preferential interactions with TS

Proteases and peptidases

– chymotrypsin, elastase, subtilisin

– reactive serine nucleophile

• Some aldehyde dehydrogenase

– glyceraldehyde-3phosphate dehydrogenase

– reactive thiolate nucleophile

• Aldolases and decarboxylases

– amine nucleophile

• Dehalogenases

– carboxylate nucleophile

Enzyme Kinetics

Enzymes affect rates but not equilibria

• Reactions are Complex – Simplifying

assumptions

Michaelis-Menten kinetics

Total Enzyme concentration is fixed