1A: Acids, Bases, Buffers, Oh My!

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Areas of Biochemistry:

Structural & Functional:

Chemical structures and 3D arrangements of molecules

Bioenergetics: The flow of

energy in living organisms and how it is transferred from one process to

another

Key Definitions:

Intermolecular

Forces: hold

molecules together inside of the cell

Dipole:

separation of charge

Ka: how much acid has dissociated; indicates

acid's strength (ie. the larger the number, the more product that's produced,

the more dissociation that has taken place, the stronger the acid)

pKa: pH where 50% of the

protons have come off

pH: -log[H+] ; free [H+]

Hypercapnia: too much CO2 in lungs

Hypoventilation: too little CO2 being

expelled (breathed out)

HA:

acid, a proton and its conjugate base

H+:

proton released when acid dissociates in water (also H3O)

A-:

the conjugate base

General Notes

Relationships between

processes are key. Might be a good idea to go through and find

relationships as we are taught more processes

We won't be covering Nucleic

Acid stuff

Amides- Sp2 HYBRIDIZED

b/c resonance

Resonance limits rotation,

and in this case prevents it entirely ---> makes shape important

Higher bp/mp means that the

forces are harder to pull apart and are thus stronger

Higher bp/ lower mp means

that the forces are easier to pull apart and are thus weaker

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4 Major Classes of Biomolecules:

Macromolecule

Monomer

Linkage

Protein

Amino acid

Peptide (amide)

Polysaccharide

Monosaccharide

Glycoside (acetal)

Lipids

Fatty acids

Ester

Nucleic Acids

Nucleotide

Phosphodiester

Intermolecular Forces:

Ion Interactions

Ion- dipole: between an ion

and a molecule with a dipole

Hydrogen bond: (FON)

Dipole-dipole/ ion-ion:

between two dipolar molecules or two ions

Dipole-induced dipole: the

dipole of one molecule induces a dipole in a non-polar molecule

Dispersion forces: in every

molecule

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Acids and Bases:

pKa

Ka

Smaller pKa--> stronger

acid

Larger pKa--> weaker

acid (stronger conj. Base)

pKa= -log(ka)

Large Ka--> strong acid

This means the substance

has been mostly dissociated into H+ and base (A-), and that there is

not much HA left

This occurs when

numerator is large, and denominator is small

Reaction will shift to side

with weaker acids/bases

So this means the reaction

will shift to the side with the bigger pKa

Buffers:

Best buffers have equal

concentration of acid and conj. Base

If more H+ is added…

Equilibrium shifts to the

side the acid is on

Why?

Because the added H+ will

react with the conj. Base and make more acid

When you add acid, you'll

make more acid

If base is added…

Equilibrium shifts to the

side the base is on

Why?

Because the added base will

react with the conj. Acid and make more base

When you add base, you make

more base

The [H+] doesn't change very

much, but the ratio does

The Henderson-Hasselbalch

equation explains how buffers work

Add acid that will react with

A- to make more HA

Add base that will react with

HA to make more A-

Three Major Physiological Buffer Systems:

Protein Buffer System: helps

regulate pH in ECF and ICF; interacts extensively with other buffer

systems

Carbonic Acid Bicarbonate

Buffer System: most important in ECF

Phosphate Buffer System:

buffers pH of ICF and urine

The Carbonic Acid Bicarbonate :

Carbonic Acid: H2CO3

Bicarbonate: HCO3-

Used because you can regulate

it

HOW?????

Carbonic Anhydride catalyzes

dissociation of Carbonic Acid into H+ and HCO3-

You can remove CO2 from blood

(breathing) to increase pH (more basic)

You can remove HCO3- from

blood (vomiting, urinating) to lower the pH (more acidic)

This can result in two

conditions if taken too far…

What happens if your body

strays from its happy pH??

Acidosis

Alkalosis

Blood pH decreases

Becomes acidic

[H+] increases

Too much CO2

Blood pH increases

Becomes basic

[H+] decreases

Not enough CO2

Respiratory Acidosis:

Cause: body can't get rid of

CO2

Signs: low plasma pH from

hypercapnia

[CO2] increases, equilibrium

shifts to opposite side of CO2 (side with Bicarbonate) and pH goes down

(acidic)

Metabolic Acidosis:

Cause: production of large

numbers of fixed or organic acids (lactic acidosis from anaerobic cell

respiration); Ketoacidosis (excess ketone bodies from starvation,

untreated diabetes); too much alcohol; excessive loss of bicarbonate ions;

impaired kidney function

Bicarbonate concentration

drops, equilibrium shifts toward bicarbonate

Respiratory Alkalosis

Cause: hyperventilation

Signs: elevated pH due to

hypocapnia

[CO2] decreases, equilibrium

shifts toward side with depleted CO2, conc. of H+ decreases, pH goes up

(basic)

Metabolic Alkalosis:

Cause: gain [HCO3-] or loss

H+

Add bicarb

Loss of fluids with low

bicarb

Loss of hydrogen

Loss of 1 H = addition of 1 bicarb

Bicarb concentration

increases, system shifts to make more CO2,

H+ conc decreases, pH rises (basic)

Hemoglobin Buffer System

Hemoglobin buffers CO2 and H+

CO2 diffuses across RBC

membrane from tissue

20% CO2 binds directly with

hemoglobin and is released into lungs

70% of CO2….

Reacts with water and forms

carbonic acid

Inside of the RBC, carbonic

acid dissociates into bicarbonate

Bicarb ions diffuse into

plasma as Cl- ions diffuse from plasma into RBC

H+ then can bind to

hemoglobin and be released in the RBCs in lungs to combine with bicarb

CO2 reformed for exhalation

in lungs

Buffers in Kidneys

Only kidneys can get rid of

metabolic acids

Ie) H+ and bicarb

Help us to eliminate large

amounts of H+ in a normal volume

Acidotic conditions: kidneys

excrete H+ and retain bicarb

Alkalotic conditions: kidneys

retain H+ and excrete bicarb

Slower process than

breathing, but more powerful because it lasts longer

Buffers in Urine

Carbonic Acid-Bicarbonate

Buffer System

Phosphate Buffer System:

H2PO4 (weak acid) and HPO4 (conj. Base)

Ammonia Buffer System: bicarb

is reabsorbed along with Na+