Exam 1 Biochem Flashcards
Transcription
DNA copied into complementary RNA
Translation
Adding nucleotides to ribosomes to grow polypeptide chain
Most common essential elements for life
C, H, N, O, P, S
Metal ions essential for life
K, Na, Ca, Mg, Zn, Fe, V, Cr, Mn, Co, Ni, Cu, Mo, W, Se, I
ABCs of Life
(A) Amino acids
(B) Components of Nucleic Acids
(C) Components of lipids
Components of Nucleic Acids
Nitrogenous bases (U/T, C, A, G)
5 Carbon sugars (Ribose or deoxyribose)
Phosphate (PO4H2)
Stereoisomers function and properties
have different physical properties from each other
Components of lipids
–Phosphate
–Glucose
–Carbon backbone
Geometric isomers function and properties
(cis vs. trans or across double bonds)
have different physical and chemical properties
Enantiomers (mirror images)
isomers function and properties
have identical physical properties (except with regard to polarized light) and react identically with achiral reagents
Diastereomers (non-mirror images)
isomers function and properties
have different physical and chemical properties
entropy
As the entropy of the universe increases, creating and maintaining order requires work and energy.
How to Speed Reactions Up and Limitations (4)
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
endergonic
Synthesis of complex molecules and many other metabolic reactions requires energy
exergonic
The breakdown of some metabolites releases a significant amount of energy
Why are some reactions endergonic?
A reaction might be thermodynamically unfavorable (delta G°> 0).
Creating order requires work and energy.
A metabolic reaction might have too high an energy barrier (delta G‡ > 0).
Metabolite is kinetically stable.
How might some reactions be exergonic?
Such metabolites (ATP, NADH, NADPH) can be synthesized using the energy from sunlight and fuels.
Their cellular concentration is far higher than their equilibrium concentration.
Energy Coupling
allows otherwise unfavorable reactions to occur
Catalysis
a compound that increases the rate of a chemical reaction.
Catalysts lower the activation free energy G‡.
Catalysts do not alter G°.
Enzymatic catalysis offers:
acceleration under mild conditions
high specificity
possibility for regulation
Why is water the medium for life?
Life evolved in water (UV protection!)
Organisms typically contain 70–90% water.
Chemical reactions occur in aqueous solutions.
Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes.
Structure of the Water Molecule
-Four electrons around O
-Four sp3 orbitals
-O covalently bonded to H2
-2 lone pairs nonbonding
-VESPR is bent
-EN of oxygen is a net dipole
-Water is both H bond donor and acceptor
Hydrogen Bonds
Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a covalently bound hydrogen and lone pair of electrons.
They typically involve two electronegative atoms (looking for H connected to F,O, or N).
Hydrogen bonds are strongest when the bonded molecules allow for linear bonding patterns. (3 atoms hopefully)
Up to four H-bonds per water molecule gives water its what three properties?
anomalously high boiling point
anomalously high melting point
unusually large surface tension
Energy values of H2O bonds
Hydrogen bonds between neighboring molecules are weak (20 kJ/mol) relative to the H–O covalent bonds (420 kJ/mol)
Ice: Water in a Solid State
different crystal forms; the hexagonal ice is the most common.
Hexagonal ice forms an organized lattice and thus has a low entropy.
maximal hydrogen bonds/ water molecules in equidistant arrangement (ice floats!!)
Water is a good solvent for…
charged and polar substances:
-amino acids and peptides
-small alcohols
-carbohydrates
Water is a poor solvent for
nonpolar substances:
-nonpolar gases
-aromatic moieties
-aliphatic chains
Noncovalent Interactions
Ionic (Coulombic) interactions
Dipole interactions
van der Waals interactions
Hydrophobic Effect
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 nonpolar substances
van der Waals Interactions
-attractive force (London dispersion), which depends on the polarizability
-repulsive force (Steric repulsion), which depends on the size of atoms
Attraction dominates at longer distances (typically 0.4–0.7 nm).
Repulsion dominates at very short distances.
Biochemical Significance of van der Waals Interactions
Weak individually
Universal
Importance
-determines steric complementarity
-stabilizes biological macromolecules (stacking in DNA)
-facilitates binding of polarizable ligands
The Hydrophobic Effect
association or interaction of nonpolar molecules or components of molecules in the aqueous solution
Is one of the main factors behind:
protein folding
protein-protein association
formation of lipid micelles
binding of steroid hormones to their receptors
Does not arise because of some attractive direct force between two nonpolar molecules
Solute Effects on Colligative properties of Water:
-boiling point, melting point, and osmolarity
-do not depend on the nature of the solute, just the concentration
Solute Effects on noncolligative properties of Water:
-viscosity, surface tension, taste, and color
-depend on the chemical nature of the solute
Osmotic Pressure (Concentration effects)
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.
Cell in isotonic solution
No net water movement
Cell in hypertonic solution
Water moves out of cell and cell shrinks
Cell in hypotonic solution
Water moves in creating outward pressure, cell swells and may burst
Ionization of Water
H20 ««—> OH - and H+
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
Low Keq Value
Proton Hydration
Protons do not exist free in solution.
They are immediately hydrated to form hydronium ions (H3O)
The covalent and hydrogen bonds are interchangeable. This allows for an extremely fast mobility of protons in water via “proton hopping.”
Dissociation of Weak Electrolytes: Principle
Weak electrolytes dissociate only partially in water.
The extent of dissociation is determined by the acid dissociation constant Ka.
We can calculate the pH if the Ka is known. But some algebra is needed!
Buffers
Mixtures of Weak Acids and Their Anions (Conjugate Base)
Buffers resist change in pH.
pH = PK
1:1 mix of acid/base
Henderson–Hasselbalch Equation: Derivation
Know it
Maintenance of intracellular pH is vital to all cells.
Why?
Enzyme-catalyzed reactions have optimal pH.
Solubility of polar molecules depends on H-bond donors and acceptors.
Equilibrium between CO2 gas and dissolved HCO3– depends on pH.
Buffer systems in vivo are mainly based on:
phosphate, concentration in millimolar range
bicarbonate, important for blood plasma
histidine, efficient buffer at neutral pH
Buffer systems in vitro are often based on sulfonic acids of cyclic amines.
Sulfur is often not used metabolically by bacteria so buffer systems last longer!!
