Foundations of Biochem Flashcards
non covalent chemical reactions, eg and function
chemical side roots of one molecule interact with chemical side root of other
eg: protein, dna, lipids, carbs
function: stabilise structure, allows hormones to bind to receptors, match chemicals
chemistry of life - 4 key concepts
- molecular complementarity: allows protein with complementary shapes/chemical properties to interact
- small molecules form larger cellular structures (monomers form polymers) eg DNA
- chemical reactions are reversible
- energy driving cellular activities is derived from ATP hydrolysis
4 types of macromolecules and 3 levels (monomer, polymer and cell structure)
M –> P –> CS
- AA –> polypeptide –> protein filament
- nucleotide –> DNA strand –> chromosome
- monosaccharide –> starch –> starch grangule
- FA –> triacyl-glycerol –> fat droplets
Role of carbon/carbon bonding
Carbon can form covalent, single, double or triple bonds -versatile. carbon participates in numerous bonds important for sustaining life - found in all macromolecules of the body.
essential elements
C, H, O, N, P, and S Metal ions (e.g., K+, Na+, Ca2+, Mg2+, Zn2+, Fe2+) play important roles in metabolism.
molecule function
function of molecule strongly dependent on 3D structure - structure determines function.
types of isomers
Stereoisomers: have different physical properties
Geometric isomers (cis vs. trans): have different physical and chemical properties
Enantiomers (mirror images): have identical physical properties (except with regard to polarized light) and react identically with achiral reagents
Diastereomers (non-mirror images): have different physical and chemical properties
interactions between biomolecules
Interactions between biomolecules are specific (key concept)
Macromolecules fold into 3D structures with unique binding pockets (eg active site, subtrate etc)
Interactions between molecules determined by 3D molecular structure of the molecules
Only certain molecules fit in well and can bind. Binding of chiral biomolecules is stereospecific.
Eg Proteins, receptors, hormones, enzymes
factors that increase reaction rate
Higher temperatures: stability of macromolecules is limiting
Higher concentration of reactants: costly, as more valuable starting material is needed
Changing the reaction by coupling to a fast one: universally used by living organisms
Lower activation barrier by catalysis: universally used by living organisms
unfavourable vs favourable reactions
Synthesis of complex molecules and many other metabolic reactions requires energy (endergonic).
o A reaction might be thermodynamically unfavorable (ΔG°> 0). Creating order requires work and energy.
o A metabolic reaction might have too high an energy barrier (ΔG‡ > 0). Metabolite is kinetically stable.
The breakdown of some metabolites releases energy (exergonic).
o Such metabolites (ATP, NADH, NADPH) can be synthesized using the energy from sunlight and fuels.
o Their cellular concentration is far higher than their equilibrium concentration.
endergonic: non spont, unfav, +ve ΔG°, req E
exergonic: spont, fav, -ve ΔG°, releases E
energy coupling
Chemical coupling of exergonic and endergonic reactions allows otherwise unfavourable reactions.
The “high-energy” molecule (ATP) reacts directly with the metabolite that needs “activation.”
catalysis
A catalyst is a compound that increases the rate of a chemical reaction.
- lower the activation free energy ΔG‡.
- Catalysts do not alter ΔG°.
- Enzymatic catalysis offers: acceleration under mild conditions (eg human cell, 37ºC, neutral pH – mild cond). high specificity (only regulate one reaction), and possibility for regulation (self regulation)
function of water
Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes.
- organisms contain ~70% water
structure of water
dipolar, tetrahedral arrangement of outer shell e- with O atom. 2xH+ atoms have δ+ and O has δ- allowing formation of H bonds
hydrogen bonds
strong dipole-dipole or charge-dipole interactions, arise between covalently bound hydrogen and lone pair of e-.
- usually H-O or H-N
importance of H bonding
- Source of unique properties of water
- Structure and function of proteins
- Structure and function of DNA
- Structure and function of polysaccharides
- Binding of substrates to enzymes
- Binding of hormones to receptors
- Matching of mRNA and tRNA
H bonding in water
Water can serve as both:
o H donor
o H acceptor
Up to four H-bonds per water molecule gives water its:
o anomalously high boiling point
o anomalously high melting point
o unusually large surface tension
Hydrogen bonds between neighboring molecules are relatively weak (20 kJ/mol)
H–O covalent bonds are strong (420 kJ/mol).
water as a solvent
good solvent for charged and polar substances (eg AA, alcohols, CHO)
poor solvent for nonpolar solvents (eg non polar gases, lipids)
non covalent interactions
do not involve sharing of a pair of e- o Ionic interactions o Dipole interactions (H bonds) o van der Waals interactions o Hydrophobic Effect
ionic interaction
electrostatic interactions between permanently charged species, or between the ion and a permanent dipole
dipole interactions (H bonds)
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
- Attraction dominates at longer distances
- Repulsion dominates at very short distances.
- There is a minimum energy distance (van der Waals contact distance).
hydrophobic effect
Refers to the association or interaction of nonpolar molecules or components of molecules in the aqueous solution
Is one of the main factors behind:
o protein folding
o protein-protein association
o formation of lipid micelles
o binding of steroid hormones to their receptors
- Does not arise because of some attractive direct force between two nonpolar molecules - More a case of associating to “avoid” the aqueous (water) environment.
osmotic pressure
Water moves from areas of high-water concentration (low solute concentration) to areas of low water concentration (high solute concentration).
Osmotic pressure (π) is the force necessary to resist the movement.
- Influenced by the concentration of each solute in solution.
- Dissociated components of a solute individually influence the osmotic pressure.
ionisation of water
H20 H+ + OH-
O-H bonds are polar and can dissociate heterolytically. Products are a proton (H+) and a hydroxide ion (OH–).
Dissociation of water is a rapid reversible process.
Most water molecules remain un-ionized, thus pure water has very low electrical conductivity.
The equilibrium is strongly to the left (low Keq).
The extent of dissociation depends on the temperature.
proton hydration
protons do not exist free in solution, they are immediately hydrated to form H3O+ ions.
H3O+ are solvated by nearby water molecules.
pH equations
pH = -log[H+] Kw = [H+][OH-] = 1x10^-14
dissociation of weak electrolytes
Weak electrolytes dissociate only partially in water.
The extent of dissociation is determined by the acid dissociation constant Ka
- Ka = how easily molecules separate into components
We can calculate the pH if the Ka is known.
pKa
pKa = -logKa
pKa was introduced as an index to express the acidity of weak acids, where pKa is defined as the negative log of the dissociation constant. A lower pKa value indicates a stronger acid. That is, the lower value indicates the acid more fully dissociates in water.
Pka indicator of how readily will donate protons, smaller pka = stronger acid
buffers
Mixtures of weak acids and their conjugate bases
Buffers resist change in pH
At pH = pKa, there is a 50:50 mixture of acid and anion forms of the compound.
Buffering capacity of acid/anion system is greatest at pH = pKa.
- Buffering capacity is lost when the pH differs from pKa by more than 1 pH unit. (once enough acid is added, the buffer is overwhelmed and broken)
titration curve of acetic acid
At the midpoint of the titration, the concentrations of the proton donor and proton acceptor are equal, and the pH is numerically equal to the pKa. The shaded zone is the useful region of buffering power, generally between 10% and 90% titration of the weak acid.
biological buffer systems
Maintenance of intracellular pH is vital to all cells.
o Enzyme-catalyzed reactions have optimal pH.
o Solubility of polar molecules depends on H-bond donors and acceptors.
o Equilibrium between CO2 gas and dissolved HCO3– depends on pH.
