Biochem exam 1 (ppts 2-4) (Water, Amino acids and peptides, and 3-D structure of Proteins.)

is water polar or nonpolar

polar

is water a covalent or ionic bond

covalent

what is the 3D structure of water?

tetrahedral

__ is more electronegative than __. It draws electrons towards itself 

O2; H+

Water is considered a __pole

di

water dissolves __ and __.

low MW polar (hydrophilic) compounds; ionic solutes

what kind of bonds does water form

Hydrogen bonds

there is __ attraction between d-O and d+H

electrostatic

hydrogen bonds are__, but__

weak; additive

water forms hydrogen bonds with

solutes

In liquid water, at room temperature and atmospheric pressure, each water molecule hydrogen-bonds with an average of __ other water molecules

3.4 (~4) 

how many hydrogen bonds are created on each water molecule

4 hydrogen bonds

after 4 hydrogen bonds are created, what kind of crystal is made in water

lattice crystal

lattice crystal makes ice __ dense than water

less

covalent bonding is a major stabilizing factor in

organic compounds

covalent bonding holds

atoms in geometric forms

non-covalent bonding stabilizes and organizes

forces in nature

non-covalent bonding include which kinds of bonds

ionic bonds, hydrophobic forces/interactions, and hydrogen bonds, Van der Waals Interactions (Dispersion forces)

ionic bonding is also called

salt bridge, salt linkage, ion pair

ionic bonds are 

electrostatic attractions between oppositely charged ions

Hydrogen bonds are not unique to water. They are also needed for

cell replication and transcribe DNA

H-bonds are weak and needed to __ DNA strands held together by H-bonds

unwind

Hydrogen bonds are attractive interactions between dipoles when the (+) end of a dipole is an

H atoms bonded to an atom of high electronegativity (most commonly O, N, or C)

Hydrogen bonds are attractive interactions between dipoles when the (-) end of a dipole is an

atom with a lone pair of electron (most commonly O or N)

Hydrophobic forces/interactions

forces that hold non-polar regions of molecules together 

Hydrophobic forces/interactions result from

the tendency of water to exclude hydrophobic groups 

Hydrophobic forces/interactions are ___ than H-bonds

weaker

amphipathic compounds contain regions that are

polar and nonpolar

when amphipathic compounds is mixed with water, the polar (hydrophilic) region

interacts with solvent and tends to dissolved

when amphipathic compounds is mixed with water, the non-polar (hydrophobic) region

tends to avoid contact with water

micelles (stable structures of amphipathic compounds in water)

nonpolar regions of molecules cluster together to present smallest hydrophobic areas to aqueous solvent- while polar regions are arranged to maximize their interactions with the solvent

van der waals interactions are also called

dispersion forces

van der waals interactions are

attractive forces between 2 atoms when 3-4 amino acids apart

As 2 nuclei draw closer together their

electron clouds being to repel each other- but van der waal interactions balance the repulsive forces 

when van der waal interactions balance repulsive forces between two nuclei they are in

van der waal contact

the CH₃COOH is the __, and the CH₃COO^- __

conjugated acid; conjugated base

before any base is added to the acid, the pH of the solution is fairly

low

the best buffering capacities of the solutions are

±1 pH units from the pKa

Buffers are

aqueous solutions that tend to resist changes in pH when small amounts of acid or base are added

Buffer DO NOT

prevent changes in pH

Buffers are the effective __ pH unit from pKa

±1

buffer have __ capacities

limited

maximal buffering capacities when

pH=pKa

the ability to prevent changes in pH is directly proportional to the total 

acid and base

a buffer consists of a __ plus its conjugated base

weak acid

a buffer consists of a __ plus its conjugated acid

weak base

What happens to the equilibrium as H⁺ is added?

H⁺¹ reacts with the base and shifts the equilibrium to the left increasing the [H₂PO₄^-1].

What happens to the pH as H⁺ is added?

There still a decrease in pH, since the [HPO₄^-2]/[H₂PO₄^-1] decreases.

The maximum buffer efficiency is when [HPO₄^-2]/[H₂PO₄^-1]   =

1

the only pK relevant at physiological conditions is

6.85

water has a small degree of __ (reversible)

ionization

ionization of water is crucial for

cellular functions

what is depicted on this image

ionization of water

what is depicted on this image

the equilibrium constant of water

the equilibrium constant formula is __ over __

reactants; products

at room temperature (25C), what is the molality of H2O

Keq = 55.5M

what is the Kw (ion-product constant) of water

1 × 10^-14

When   [H⁺] = [OH^-]  =  1 X 10^-7 , pH is

7, neutral

the ion production of water is the bases for

the pH scale

the pH formula is

pH= -log [H+]

pOH + pH =

14

pH affects the __ and __ of macromulecules

structure; activity

the more H there is in a solution, the less __ is in a solution

OH

the more OH there is in a solution, the less __ is in a solution

H

HCl and HNO3 are examples of

strong acids

strong acids __ ionize in a solution

completely

weak acids __ ionize in a solution

partially

KOH, NaOH are examples of

strong bases

bronsted acids are proton __

donor

bronsted bases are proton __

acceptors

what is depicted here

a bronsted acid and a brosnted base

HA represents

the conjugated acid

A- represents

a conjugated base

HA and A- are only different by _ proton

1

how would you write the Ka of

Ka  =   [CH₃COO^-]  [H₃O⁺]     

                   [CH₃COOH]                                    

Ka is

dissociation (ionization) constant for a given acid when temperature is constant

The greater the Ka, the __ the acid

stronger

The smaller the Ka, the __ the acid

weaker (ka)

pKa formula, pKa=

-log(Ka)

the smaller the pKa, the __ the acid

stronger (pka)

the higher the pKa, the __ the acid

weaker (pKa)

The pH of a solution is solely dependent on the __ of the conjugate acid and base

equilibrium concentrations

The__ of a solution is solely dependent on the equilibrium concentrations of the conjugate acid and base

pH

Henderson-Hasselback equation 

pH  = pKa  + log [conj base] 

                           [conj acid]

In the Henderson-Hasselback equation the pH is equal to the pKa + the log of the __ over the __

conjugated base; conjugated acid

when a base=acid

the pH=pKa

when the pKa=pH

a base=an acid

maximum buffering capacity is when

pH = pKa then a base=an acid

Henderson/Hasselback equation only applies to __ acids and bases

weak

the pKa of an acid is the pH at which and acid is__ ionized

half

since pKa of an acid is at a given temperature constant, the pH changes require changes in 

base/acid

when pH less than pKa, the __ predominates

acid

when pH greater than pKa, the __ predominates

base

when the acid predominates

H+ is on

when the base predominates

H+ is off

amino acids are the building

blocks of proteins

Human have enzymes to synthesize __ out the 20 biologically important amino acids

11

the 9 essential amino acids

Arg, His, Ile, Leu, Trp, Lys, Met, Phe,Thr and Val

Arg is essential only in 

rats and newborn babies

amino acids are precursors in the ___ of other amino acids

synthesis