Lecture 1 Flashcards by Andres Nunez

Why is carbon so central in biomolecules?

C-C strongs are strong (unlike Si-Si bonds)
C forms multiple stable bonds which can lead to structural diversity
C-N and C-O bonds are stable but still reactive enough to form new compounds

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Amide bonds are ___

Strongly polarized

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What is an Imidazole?

R-the cyclopentene in tryptophan

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What is an Imidazolium?

R-Imidazole but the N without an H gains one and gains a + charge

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What is a Thiol?

R-SH

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What is a disulfide bond?

R1-S-S-R2

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What is a thiolate?

R-S^-

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What is a imine (Schiff base)?

R-N–C-R1+R2

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What is a thioester?

Ester but replace a S with the loose O

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What is an anhydride?

Two esters that share the O

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What is a mixed anhydride (Acyl Phosphate)?

Ester that connects the loose O to a phosphate group

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Enantiomers have identical physical and reactive properties with respect to ____ reagents

Achiral

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Do diastereomers have the same physical and chemical properties?

Nope

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What is a Bronsted Acid & Base?

Acid - proton donator
Base - proton acceptor

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What is a Lewis Acid & Base?

Acid - electron pair acceptor
Base - electron pair donator

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In an alpha helix, all amino acids have the same ___

Chirality

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How can protonation state affect electrostatic potentials?

Can make molecules + or -

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What is Gibbs Free Energy (G)?

Energy of an entire system at constant P; measurement of maximum work

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At constant P and V, what is H?

deltaH=q

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When deltaG is greater than 0, what is that called? Is products or reactants favored?

Endergonic, reactants

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When deltaG is less than 0, what is that called? Is products or reactants favored?

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Exergonic, products

What does deltaGrxn equal at equilibrium? Therefore what does deltaG0rxn =?

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0
deltaG0rxn = -RTlnKeq

What is the definition of Gibbs free energy? (equation)

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dG0rxn = dH0rxn - TdS0rxn

For more complex reactions, what does dGrxn =?

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dG0rxn + RTlnQ

What is the biochemist version of dG0 and what makes it different?

dG'0 It differs as this defines the reaction at pH=7, H+ activity = 1, and for dilute solutions, H2O activity = 1

What does the free energy of ATP hydrolysis help ATP do?

Act as a phosphate donor and as an energy source to drive reactions (through Hess' Law)

What is Kw?

[H+][OH-]

What is the Henderson-Hasselbach equation?

pH = pKa + log[A-]/[HA]

What might affect a functional groups pKa?

A neighboring functional group

What has more of an effect on pKa, a charged & eneg group or a nonpolar group?

Charged & eneg group

What is an coulombic (electrostatic) interactions?

Electrostatic intereactions between charged species, between ions and permanent dipoles, between two dipoles, and even between quadrupoles Non-covalent interaction

What are hydrogen bonds?

Strong dipole-dipole or charge-dipole interaction that arises between an acid and a base Non-covalent interaction

What are Van der Waals Interactions?

Weak interactions between all atoms, regardless of polarity - attractive (dispersion) and repulsive (steric component) Non-covalent interaction

What are the three electrostatic interactions?

- Ion-Ion Interactions - Ion-Dipole Interactions - Dipole-Dipole Interactions

What is the hydrophobic effect?

Phenomenon associated with the ordering of water molecules around non-polar substances Non-covalent Interactions

Non-bonded interactions dictate__________

biomacromolecule folding/association, cellular compartmentalization, drug binding, and enzyme catalysis

What are Ion-Ion Interactions?

Attraction or repulsion between point charges, depends on separation and dielectric of medium E = q1q2/4piee0r

What are ion-dipole interactions?

Depends on length and orientation of dipole

What are dipole-dipole interactions?

All dipole interactions for dipoles of fixed orientation on timescale of the interaction, r > I1 or I2

What is the strongest kind of H-bond?

Charged H-bond

What are the two components of van der Waals interactions?

Attractive force (LDF) - depends on polarizability of atoms Repulsive force (Steric repulsion) - depends on the size of atoms

What dominates at longer distances, attraction or repulsion? How about vise versa?

Long distance - attraction Short distance - repulsion

In strong hydrogen bonds, heavy atom ________ interpenetrate

Van der Waals radii

Water has

- high e - anomalously high boiling point - anomalously high melting point - unusually large surface tension

Water forms ____ transiently in solution phase

Ice-like latttice

What are the signs of dH and dS when water becomes ordered around lipids?

dH ~ 0 dS < 0

What are the signs of dH and dS when lipids aggregate and water is released?

dH ~ 0 dS > 0

What are the signs of dH and dS when a micelle forms?

dH < 0 dS > 0

Where are hydrophobic amino acids in a protein structure?

Often in the protein core

What are cation-pi interactions?

Cations binding to the elctron rich faces of benzene or other pi systems

Aromatic group can act as a ____ that can be buried in areas of proteins where a ___ is _____

Hydrophobic anion anion Destabilizing

Lecture 1 Flashcards

(52 cards)