biochem exam 1

Covalent bond

The bond between two atoms sharing one or more pairs of electrons

Ionic bond

Electrostatic attraction between oppositely charged species

Hydrogen bond

A dipole-dipole interaction occurring between a hydrogen covalently bound to an N, O, or F atom (donor) and another N, O, or F atom (acceptor).

Electronegativity

The ability of an atom to attract electrons to itself in a bond

Dipole

A concentration of positive electric charge separated from a concentration of negative charge, often due to differences in the electronegativity of atoms

van der Waals interactions

Weak, short-range, electrostatic, attractive forces between uncharged molecules arising from dipole moments. If atoms get too close, the van der Waals force becomes repulsive

Van der Waals radius

An imaginary hard sphere representing the distance of closest approach for another atom (the closest two atoms can get without repelling each other)

What are the most abundant elements in the human body

O, C, H, N

What elements account for > 99% of the elements in the human body by mass

C, H, O, N, P, Ca

What helps transports oxygen and aids in DNA repair and synthesis

Fe

What elements are involved in electron transport

Fe and Cu

Covalent bonds are

the strongest and longest-lasting interaction but are rare in protein-ligand binding because we want the interaction to be reversible

Ionic bonds are

electrostatic interactions between a negatively charged species and a positively charged species

Oxygen atoms are often part of…

negatively charged functional groups, such as a deprotonated carboxylic acid

Amines and other nitrogen-containing compounds are…

common positively charged functional groups

Hydrogen bonds are

common receptor-ligand interaction occurring between a donor and a receptor

Donors need to have…

a hydrogen covalently bound to an electronegative atom

Acceptors need to have…

a lone pair of electrons to interact with the donated hydrogen

The strength of a hydrogen bond depends on…

the electronegativity of the covalently bound atom, the distance between the donor and acceptor, and their geometry (180 degrees is preferred)

A dipole is when…

a concentration of positive electric charge is separated from negative charge

Homeostasis is a…

Highly ordered steady state that requires energy and delays equilibrium

Equilibrium is when…

Homeostasis is no longer maintained and macromolecules tend to equilibrate to their surroundings

What are the four main classes of biomolecules

Amino acids, nucleotides, simple sugars, and fatty acids

What is R-NH3+

Amino

What is R-O-H

Hydroxyl

What is R-S-H

Sulfhydryl

What is R-PO3 2-

Phosphoryl

What is RCO2-

Carboxyl

What is R-CH3

Methyl

Biological systems rely on carbon bonding because of

Its versatility

Shorter bonds are…

Stronger

C-C single bond is comparable to…

C-O, Si-O, P-O, and S-H bonds

C-C single bond is weaker than…

C-H, O-H, N-H, H-H, H-Cl, C-F, and many double or triple bonds

A carbon atom can bind up to _ single bonds to form a _

4, tetrahedron

Why can single bonds rotate but double bonds cannot

The rotation around a single bond is very easy due to its sigma bond, whereas a carbon-carbon double bond includes a pi bond and rotation is not possible without breaking the pi bond

Covalent bond polarity is dependent on differences in

Electronegativity

Atoms that form polar covalent bonds have

Partial charges

Water forms H bonds with…

Polar molecules and other water molecules

Why is it important that weak forces occur in biomolecular reactions

If the bonds between biomolecules were strong, it would require a lot of energy to break them and the rate of breaking and reforming bonds wouldn't be sufficient to the dynamic interactions that characterize living processes

Ionic bonds don't share electrons, they…

either gain or lose electrons

When an ionic bond forms between sodium (a metal) and chlorine (a non-metal) when…

sodium transfers its single valence electron to chlorine

Ionic compounds form a , while the water creates a around each ion preventing the ions from rejoining the crystal

Lattice, hydration layer

Hydrophobic effects occur…

When nonpolar molecules associate in water

Hydrophobic effects _ form H bonds with water and play an important role in _

Do not, protein folding reactions

What is the importance of strong bonding versus weak bonding

Strong covalent bonds hold together permanent structures and weak interactions hold together things that must come apart repetitively and quickly

What is the relative order of oxidation for alcohols

Alcohol, Aldehyde, Carboxylic acid, carbon dioxide OR alcohol, ketone

What is the first law of thermodynamics

Energy cannot be created or destroyed

What is a system

A part of the universe you define

What are surroundings

everything else in the universe that isn't the system

What is heat

a transfer of energy between two objects due to a temperature gradient

What is work

a force acting over a distance to move an object

Heat and work are the modes by which a system can…

exchange energy with its surroundings

Chemical bonds contain

Potential energy

What is S in thermodynamics

Entropy

What is H in thermodynamics

Enthalpy

What is G in thermodynamics

Gibbs free energy

Define entropy

disorder in the system

Define enthalpy

Heat content of the system

1. What does negative enthalpy mean? 2. What does positive enthalpy mean?

1. Heat released, exothermic. 2. Heat absorbed, endothermic

Define Gibbs free energy

amount of energy from a reaction that can do work

What is the Gibbs free energy equation

deltaG = deltaH - TdeltaS

What will deltaG be and is this reaction spontaneous: -deltaH, +deltaS

-deltaG, yes

When is deltaG spontaneous?

when it is negative

When is deltaH favorable

When it is negative

When is deltas favorable

When it is positive

What will deltaG be and is this reaction spontaneous: +deltaH, -deltaS

+deltaG, no

What will deltaG be and is this reaction spontaneous: +deltaH, +deltaS

-deltaG when T is high

What will deltaG be and is this reaction spontaneous: -deltaH, -deltaS

-deltaG when T is low

Define exergonic

Gibbs free energy is less than zero, spontaneous, releases energy, and favorable

Define endergonic

Gibbs free energy is more than zero, not spontaneous, absorbs energy, and unfavorable

How can an endergonic reaction become favorable

Couple it with a exergonic reaction

What is the Gibbs free energy equilibrium equation

deltaG= -RTlnKeq

If Keq<1, deltaG is _ and it favors _

Positive, formation of reactants

If Keq>1, deltaG is _ and it favors _

Negative, formation of products

If Keq=1, deltaG is _ and it favors _

0, equilibrium

The larger the Ka, the _________ the acid because…

Stronger, protons are donated more often

Strong Acids and Bases _ in water and weak acids _

Completely dissociate, partially dissociate

What is the pH equation

pH=-log[H+]

What is the pKa equation

pKa = -logKa

What is the Ka equation

Ka=10^-pKa

Stronger acids have __ pKas

Smaller

What is the Henderson-Hasselbalch equation

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

What is the purpose of the Henderson-Hasselbalch equation?

to describe how weak acids act in solution

Buffers resist changes in pH when

small amounts of acid or base are added

In general, buffer solution is most resistant to pH change…

+/- 1 pH unit around the pKa

pH>pKa

deprotonated dominates

pH<pKa

Protonated dominates

pH=pKa

Equal mixture of protonated and deprotonated

What is the relationship between deltaG and deltaG°'

deltaG=deltaGnaught+RTlnKeq

When coupling reactions, what equation do you use?

deltaGnaught=endergonic deltaGnaught + exergonic deltaGnaught

A weak acid is titrated with a strong base. At the half-equivalence point, where exactly half of the acid has been neutralized, what does the pH equal?

The pKa of the weak acid

Two solutions are prepared at the same concentration, one of a strong acid such as HCl and one of a weak acid such as acetic acid. How do their pH values compare?

The weak acid solution has a higher pH, because it dissociates only partially

Which form of water is the densest

Liquid

Which form of water is latticed

Solid

Which form of water exists at the highest temperature

Gas

Which of the following is correct concerning the first law of thermodynamics as it applies to biological systems?

A. ΔH is less than 0 for endothermic reactions
B. The value of ΔH for a particular reaction depends on the path taken
C. ΔH is greater than 0 for exothermic reactions
D. Pressure and volume are essentially constant

D

What distinguishes the biochemical standard state from the standard state used to define standard free energy changes?

A pH of 7

True or false: Doubling the concentrations of both the weak acid and the strong acid will double the buffering capacity

True

True or false: An endergonic reaction drives an exergonic reaction in living systems

False

The pKa values usually quoted apply to acids in water. If an acidic compound is dissolved instead in a nonpolar organic solvent such as liquid hexane (C6H14), would the acid's pKa increase or decrease, and why?

The pKa would increase, because hexane cannot act as a proton acceptor