Midterm Flashcards
Why is water essential to biological systems?
- Physiochemical properties of water help form 3D shapes of biomolecules. 3D shape are related to functions.
- Water can ionize H+ and OH-. Acts as key reactant in reactions, and can also affect pH.
What is an hydrogen bond?
Electrostatic interaction between a weakly ACIDIC DONOR group (ex. O-H, N-H) and a weakly BASIC ACCEPTOR atom (ex. O, N)
How are hydrogen bonds typically drawn (represented)?
D-H ——– A
Where D = donor & A = acceptor
What are the requirements for H-bonding?
- A donor group: An H attached to an O, N, S. (positive end)
- An acceptor: An electronegative atom (O, N, S) with a lone pair. (negative end)
How many hydrogen bonds can water form?
4
2 donors, 2 acceptors
What are van der Waals forces?
NON-COVALENT associations between molecules due to ELECTROSTATIC nteractions among permanent/induced DIPOLES.
What are London Dispersion Forces?
Attractive forces between electrically NEUTRAL molecules in close PROXIMITY.
Is formed from electrostatic interactions due to the random movement of negatively charged electrons around a positively charged nucleus.
What does it mean to be hydrophilic molecule?
The molecule is polar and soluble in water. (“Water Loving”).
Contains a lot of electronegative molecules (O, N, S)
What does it mean to be a hydrophobic molecule?
Nonpolar molecule and nonsoluble in water. (“Water Fearing”).
Contains few, if any electronegative molecules (O, N, S)
Why do salts (NaCl) dissolve in water and form a salt in a nonpolar substance?
In water: water weakens attractive forces between oppositely charged ions, and hold ions apart (dissolving). The ion is attracted the charged ends of the solvent dipoles which keeps them apart. (Solvated)
In nonpolar solvents: ions attract each other so strongly that they form a solid salt.
What does it mean when ions are solvated (or hydrated in water)?
When ions in polar substances attract the opposite charged solvent dipole which surrounds the ion (like a shell) keeping it effectively apart.
What functional groups does water form hydrogen bonds with?
Hydroxyl group
Keto group
Carboxylate ion
Ammonium ion
What occurs when you add a nonpolar substance to a polar solution?
Hydrophobic effect
What is an amphiphatic molecule?
A molecule that has a distinct hydrophobic and hydrophilic portion.
What is the hydrophobic effect?
The minimization of contact by water with hydrophobic molecules by “forming” a “cage” (Clathrate cage) around nonpolar solute.
How does a nonpolar substance intrude the hydrogen bonding of water?
It ruins the network of bonds in water because it cannot donate nor hydrogen bond.
Why is the hydrophobic effect favourable when a nonpolar substance in placed in a polar solution?
It minimizes the surface area of the nonpolar solute—> maximizes H-bond ability and entropy.
Amphilies often form Micelles and Bilayers. What are micelles and bilayers?
Micelles - GLOBULES of amphiphilic molecules arranged so that HYDROPHILIC portions are on OUTer surface and HYDROPHOBIC portions in the INner core of the globule. (spheroidal aggregate)
Bilayer - A SHEET where the HYDROPHOBIC portions make up the OUTside sheet and the HYDROPHILIC in the INside. (Extended planar aggregate)
What are the three types of noncovalent interactioins that can form between water and hydrophilic biomolecules? (in decreasing strength?)
- Ionic bonds
- Hydrogen bonds
- Dipole-dipole Interactions
What type of interaction form between hydrophobic biomolecules?
London Dispersion forces.
What are ionic bonds?
An electrostatic interaction between groups of OPPOSITE charge.
What are dipole-dipole interactions?
A van der Waal reaction where an interaction occurs between an atom that has a partial positive charge and an atom that has a partial negative charge.
What do you call the condition where the pH of blood is too acidic (<7.4)?
Acidosis
What are some symptoms of acidosis?
Coma, diabetes.
What do you call the condition where the pH of blood is too basic (>7.4)?
Alkalosis
What are some symptoms of alkalosis?
Tetany
Vomiting, hyperventilation, convulsing, muscle spasms etc.
Give examples of biochemical processes that are deeply affected by pH changes.
- Transport of oxygen in the blood
- Enzymatic catalysis
- Generation of enegery in metabolic pathways
- Proteins, cells and tissues need to maintain specific pH for proper function and survival.
What is the ideal buffer range?
+-1 when pH=pKa
Why are weak acids good buffers?
It has two components:
1: Conjucate base, which absorbs H+ and buffers against acids
2. Acid, releases H+ which buffers against bases
How are bicarbonate and carbonic acid carried in blood between tissues and lungs?
O2 in lungs —> hemoglobin absorbs O2—> Releases O2 and binds H+ in muscle cell—> comes back to the lungs, releases CO2 and H20
What does the 3D structure of proteins depend on?
- presence of water
- pH
- Building blocks (amino acids)
In what configuration are amino acids in proteins?
L configuration (clockwise)
What are the three classifications of amino acids?
- Hydrophobic
- Polar (Hydrophilic)
- Charged (Hydrophilic and Charged)
List the hydrophobic amino acids
Alanine Valine Methionine Leucine Phenylalaline Glycine Tyrosine Tryptophan Isoleucine Proline
List the polar amino acids (Hydrophilic)
Serine Histidine Gluatamine Threonine Cysteine Asparagine
List the charged amino acids (Hydrophilic and Charged)
Aspartate
Glutamate
Lysine
Arginine
How can amino acids allow proteins to act as buffers?
Amino acids are weak polyprotic acids. (They contain more than one acidic proton)
Amino acids can be diprotic or triprotic
What is the difference between diprotic and triprotic amino acids?
Diprotic have neutral side chains and triprotic have an side chain that has an acidic proton