Biochem Exam 1

Covalent bond

atoms share pairs of electrons to become stable

• very strong

• ex: polar (unequal sharing) + nonpolar (equal sharing)

Noncovalent bond

no sharing of electron pairs; relies on electrostatic attractions

• weak

• ex: Ionic bonds, hydrogen bonds, and van der Waals forces

Intermolecular forces

attractive forces that act between separate neighboring molecules

• weak

• reversible

• determine physical properties e.g. melting point

Intramolecular forces

strong chemical bonds that hold atoms together inside a single molecule

• strong (involve shared or transferred electrons)

• reversible

• determine chemical properties + identity

Examples of intermolecular forces

• ion ion attractions

• dipole dipole interactions

• vander waals forces

Examples of intramolecular forces

• covalent bonds

• ionic bonds

• metallic bonds

F= (intermolecular force)

F= < -1 or > +1

• Negative (less than −1) → the interaction is attractive

• Positive (greater than +1) → the interaction is repulsive

F= (intramolecular force)

F= -1 ——> +1

• −1 = strong attraction

• Between −1 and 0 = attraction

• 0 = no net force

• Between 0 and +1 = repulsion

• +1 = strong repulsion

Ion ion attractions

the force of an electrostatic interaction between two distinct charges on atoms

• usually take place between atoms bearing a completely negative charge and positive charge

• energy of interaction is given by Coulomb’s law

Coulomb’s law

F

the force

k

proportionality constant

q₁ and q₂

charges on the two atoms

D

dielectric constant (counts for the effects of the intervening medium)

r

the distance between the two atoms (in angstroms)

What does Coulomb’s law mean?

Two atoms with opposite charges attract each other. The farther apart they are, the weaker that attraction becomes

• ex. If the distance doubles, the attraction becomes 1/4 as strong. If the distance triples, it becomes 1/9 as strong

• The material between them also affects how strong the attraction is (ex. Water)

Dielectric constant in a vacuum

D=1

• electrostatic interactions are strongest

Dielectric constant in polar environment (water)

D=80

• electrostatic interactions are weakened

Electrostatic interactions are stronger in…

nonpolar (uncharged) environment

Why does water weaken electrostatic interactions

Water can dissolve virtually any molecule that has sufficient partial or complete charges on the molecule to interact with water

• ex: NaCl is added to water → water molecules surround the ions and reduce how strongly they attract each other → ions bond to water molecules instead of each other → ionic bond is broken

rate of decrease in force for ion ion attractions

1/r²

• an ion has a full charge on it so it is still “felt” with distance → force decreases slowly

Dipole dipole interactions

attractive forces that occur when the partial positive end of one polar molecule is electrostatically attracted to the partial negative end of another polar molecule

• ex: H-bonding

Hydrogen bonding

a bond formed when two relatively e-neg atoms (O or N) unequally share a H atom that is covalently bonded to one of the electronegative atoms

• need highly e-neg atom (N, O, F)

  • hydroxyl + amino groups can H-bond

Fluorine

most e-neg atom

• not common (in lab not naturally occurring)

• used in drugs → chemotherapy

How is H bonding affected by water?

hydrogen bonding between two molecules is stronger in the absence of water

rate of decrease in force for dipole dipole interactions

1/r³

• two opposite partial charges partially cancel each other out at greater distances → force decreases faster

Hydrogen bonds in DNA double helix

bonds are weak enough to be broken by the enzymes of DNA metabolism → allowing access to the genetic information

Van der Waals Forces

electrostatic attractions between nonpolar + uncharged molecules caused by temporary shifts in electron density → at any instant charge distribution is not perfectly symmetric: regions of partial positive + negative charge

rate of decrease in force for van der waals

1/r⁶

• temporary dipoles are extremely short range so a greater distance → rapidly decreases force

Rank intermolecular forces from strongest to weakest

ion ion → dipole dipole (H-bonds) → van der waals

Entropy

measure of randomness

What happens when one benzene molecule is added to water?

benzene is nonpolar so can’t H bond with water → creates cavity in water → cavity temporarily disrupts some H bonds between water molecules → displaced water molecules reorient themselves around benzene to form max # of new H bonds → water molecules are more ordered → decreases entropy of water

What happens when two benzene molecules are added to water?

coalesce into a single large cavity → reduces amount of water that needs to be organized around benzenes → water molecules are freer to move around + have more arrangements → increases entropy

Hydrophobic effect

nonpolar molecules in aqueous solutions are driven together because of the resulting increase in entropy of water molecules

• form spontaneously → no input of energy required

How is membrane formation powered by hydrophobic effect?

phospholipid: head is hydrophilic (polar + charged), tail is hydrophobic

→ when exposed to water, molecules orient themselves such that the hydrophilic head groups interact with the aqueous medium and hydrophobic tails are sequestered away from water and interact only with one another → can form membranes stabilized by van der waals interactions

Metabolism

oxidative breakdown → break down organic molecules using oxygen to release energy

Catabolism

breakdown → release energy

• oxidation

• lose electrons

Anabolism

synthesis → consume energy

• reduction

• gain electrons

What are the 8 common functional groups?

1. hydrophobic

2. hydroxyl

3. aldehyde

4. keto

5. carboxyl

6. amino

7. phosphate

8. sulfhydryl

Hydrophobic functional group

Class of compound:

• hydrocarbon chains (aliphatic)

• aromatic

Characteristics:

• nonpolar

Hydroxyl functional group

Class of compound:

• alcohols

Characteristics:

• polar

Aldehyde functional group

Class of compound:

• aldehydes

Characteristics:

• polar

• metabolizes sugars

Keto functional group

Class of compound:

• ketones

Characteristics:

• polar

• metabolizes sugars

Carboxyl functional group

Class of compound:

• carboxylic acid

Characteristics:

• polar

Amino functional group

Class of compound:

• amines

Characteristics:

• polar

Phosphate functional group

Class of compound:

• organic phosphates

Characteristics:

• polar

Sulfhydryl functional group

Class of compound:

• thiols

Characteristics:

• polar (not as polar as hydroxyl group)

least oxidized form of carbon

hydrocarbon chains and aromatic rings

most oxidized form of carbon

CO₂

Oxidized

More oxygens

• Increase CO bonds, decrease CH bonds

Reduced

More hydrogens

• Increase CH bonds, decrease CO bonds

Nonmetal oxides in water are…

acidic

• ex: CO₂ + H₂O → H₂CO₃

  • carbonic acid releases H → more H in water = acidic

Metal oxides in water are…

basic

• ex: MgO + H₂O → Mg(OH)₂

  • magnesium hydroxide can dissociate in water producing OH → more OH in water = basic

Water ionizes to a small extent

H₂O → H⁺ + OH^-

The equilibrium constant (Keq)

Equilibrium constant of water

Keq= 10^-7 M

Ion constant (Kw)

Ion constant of water

Kw= 1.0 × 10^-14 M²

pH

[log][H+]
[H+]10^-7

Acid

proton (H) donor

Base

proton (H) acceptor

Conjugate base

chemical formed upon ionization of an acid

Conjugate acid

acid formed when a base binds a proton

Strong acid

donates all of its protons in an aqueous solution

Strong base

A base that dissociates completely into ions in solution

Weak acid

<1% dissolution in an aqueous solution

Weak base

a base that does not dissociate completely into ions in solution

Buffer

acid-base conjugate pair resists changes in the pH of a solution

• effective at a pH near its pKa

  • weak base + conjugate acid

  • weak acid + conjugate base

Henderson-Hasselbalch equation

Acids at physiological pH

base form will predominate

Bases at physiological pH

acid form will predominate

Ionizable groups

a specific part of a molecule that can gain or lose a hydrogen ion depending on the pH of the surrounding environment

• use pKa to determine change

Examples of ionizable groups

• Carboxyl group (-COOH)

• Amino group (-NH₂)

Aspirin

acetylsalicylic acid

• can deprotonate into acetylsalicylate

Role of acids and esterases in case study

catalyze the hydrolysis of esters → ester splits apart forming a carboxylic acid + alcohol

Environment of stomach in case study

highly acidic conditions (lots of H+)

• acetylsalicylic acid is predominant

Bicarbonate lavage

basic and forms acetylsalicylate from acetylsalicylic acid

• better lavage for acids

Saline lavage

salt water → neutral and will not change state of acetylsalicylic acid

• poor lavage for acids

What is the more soluble form in the case study?

the ionized form (removes as solution in the body)

Why is sodium bicarbonate lavage more effective?

sodium bicarb solution has a pH of 8.5 → more basic than stomach → causes salicylate to ionize into deprotonated/charged form → ionized form is more soluble & has a harder time crossing stomach membrane to return to bloodstream → salicylate stays dissolved in watery contents of GI tract

How does salicylate end up in blood?

acidic conditions in the stomach and esterase enzymes promote ester hydrolysis (forming salicylate)
salicylate enters the blood, which has a neutral pH (more basic), promoting deprotonation of salicylate

How does acetylsalicylic acid poisoning increase blood pH?

salicylate formation causes hyperventilation → more CO₂ exhaled → drop of CO₂ in blood → shifts reaction to the left → less H in the blood → more basic → higher pH → respiratory alkalosis

When would you use a saline solution?

if the injected chemical of concern was already in its ionic form and just needs to be flushed out

• note that stomach acid can protonate bases

Acidosis

body conditions are too acidic

• respiratory

• metabolic

Acidotic

patient affected by condition

Alkalosis

body conditions are too basic

• respiratory

• metabolic

Respiratory acidosis

not breathing properly → CO2 retention → extra CO2 reacts with H2O → will become carbonic acid → dissociates → more H → lower pH

• chronic obstructive airway disease

• severe asthma

• depression of respiratory center

• weakness of respiratory muscles

• airway obstruction

• hypoventillation

Metabolic acidosis

• Lactic acidosis  

• Severe diarrhea  

• Surgical drainage of intestine  

• Diabetis mellitis  

• Renal problems  

Lactic acidosis

low O₂ → rely on glycolysis to produce ATP → glycolysis produces pyruvate → converted to lactate → rise of H due to increased production of lactate → lowers pH

• lactate is nonvolatile → will sit in blood

Diabetes

glucose in blood but cells can’t access for energy→ body starts breaking down fat → produces ketone bodies → build up of ketone bodies → ketoacids → more H → lower pH

• can cause coma/death

• can get rid of by liver but takes a while

Respiratory alkalosis

• Hyperventilation

• Lung disease  

• Anemia  

• Salicylate poisoning

Metabolic alkalosis

• Vomiting- H+ in stomach  

• Intravenous administration of bicarb  

• Hypokalemia (low k+)  

Amino acid

compound with an amino group on one end and a carboxyl group on the other end

R group

a functional group that defines a particular amino acid and gives it special properties

Amino acid central carbon

• chiral

• forms L and D isomers

L isomer

found in our bodies, our proteins and consumed in our diet

• only L isomers are in proteins

D isomer

taken in from external sources

Essential amino acid

amino acids that we need to consume → can’t synthesize into proteins

Nonessential amino acid

amino acids that we can naturally synthesize into proteins

pKa of terminal alpha-carboxyl group

3.1