Unit 2 - Water, Weak Interactions, Order + Chaos

Biochem Exam 1

water is referred to as…

the medium for life

where did life evolve and how?

life evolved in water due to the protection it provides from UV light

organisms typically contain what range of percentages of water?

70-90%

a typical cell is what percentage of water?

70%

biochemical reactions occur in what type of solutions?

aqueous

how is water important to proteins, nucleic acids, and membranes?

water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes

covalent bonds are stronger than noncovalent bonds

true

define a covalent bond

when two nonmetal atoms share one or more pairs of electrons

draw a water molecule with its partial charges

is water polar or nonpolar?

polar

what intramolecular bonds are formed within water?

covalent bonds are formed between oxygen and hydrogen, these bonds are strong

what intermolecular bonds are formed between water molecules?

hydrogen bonds form from one water molecule to another

hydrogen bonds are not unique to water

true

hydrogen bonds are formed between what two atoms (what are the general names for them)?

• hydrogen acceptors (usually a very electronegative atom like O or N)

• hydrogen donors (usually hydrogen bonded to another electronegative atom)

hydrogen atoms bonded to this atom DO NOT participate in hydrogen bonding, why?

carbon (C-H bond is not very polar)

what does not dissolve in water?

• things that do not make hydrogen bonds (ex: oils)

• nonpolar gases are poorly soluble in water

pure water is slightly…

ionized

describe O-H bonds

they are polar and can dissociate

what are the products that water forms?

a proton (H+) and a hydroxide ion (OH-)

dissociation of water is a rapid, reversible process

true

most water molecules remain…

un-ionized (meaning they don’t dissociate)

describe where equilibrium lies with this reaction and why

equilibrium lies to the left (low K_eq) because the neutral water molecules are more energetically stable than the ionized products

oxygen is extremely…

electronegative

what type of molecule is water a good solvent for?

a charged or polar molecule

what is the maximum number of hydrogen bonds per one water molecule?

4

are hydrogen bonds strong or weak?

weak!!

why are weak, noncovalent interactions important?

they allow molecular surfaces to interact temporarily and repeatedly

weak, noncovalent bonds can be easily…

broken

think of an example when noncovalent bonds need to be broken

• noncovalent bonds are needed when DNA needs to be opened up in order to be replicated

• hydrogen bonds between adenine and thymine as well as guanine and cytosine can be broken and reformed easily because they are weak

when two atoms bond how do their charges change?

they acquire partial charges (ex: when oxygen and hydrogen bond, their full negative and positive charges become partial)

what is the hydrophobic effect?

when nonpolar molecules group together in the presence of water

give an example of the hydrophobic effect

oil droplets in chicken soup

what is the second law of thermodynamics?

the total entropy of a system and its surroundings always increases in a spontaneous process

how does entropy of water and entropy of the system change based off the aggregation of nonpolar groups in water?

• the entropy of water decreases because water has to become more ordered around the new, big, nonpolar group

• the entropy of the system increases because the water molecules that were ordered around the separated nonpolar groups become disrupted, leading to more chaos

the hydrophobic effect powers…

• membrane formation by phospholipids

• protein folding

how does the hydrophobic effect favor protein folding?

proteins fold in aqueous solutions and become more ordered

when proteins fold, what entropy change occurs, why?

there is a loss of entropy because proteins are becoming more ordered

if the pH is altered, what does this change for the organism?

alterations in pH result in drastic changes in the electrostatic environment (where electrical charges accumulate) of the organism

alterations in pH alter which interactions?

weak interactions that maintain the structure of biomolecules

an acid is a proton _________ and a base is a proton ________

donor, acceptor

define titration

the process of gradually adding known amounts of reagent to a solution to see how the reagent reacts with the solution (and monitoring the results)

what is K_a

the equilibrium constant

a larger K_a indicates a _______ ______, while a small K_a indicates a ________ _______

stronger acid, weaker acid

what does it mean if pH = pK_a

then the acid is half protonated and half deprotonated

buffers tend to resist a change in…

pH

what two things act as a buffer?

acid-base conjugate pair