Properties of Biological Molecules Flashcards
Describe Covalent bonds?
Strong
Short
Share electrons
Describe noncovalent bonds?
Weak
Long
Attraction only
What bonds make up carbohydrates?
Glycosidic
What bonds are between monomers of lipids?
Esters
Describe and give an example of an electrostatic interaction?
Charge Charge interaction between two completely charged ions, such as NaCl and ionic bond, or salt bridges. Salt bridges are interactions betweeen two amino acids in a protein.
What is Coulomb’s law used for and when using Coulomb’s Law what does F>0 and <0mean?
It is used to measure how attractive two ions are to each other. F>0 means the ions are repulsing and F<0 means they are attracted.
What is the equivalent to Coulomb’s law in a biological environment?
Relative Permittivity is added into the equation. F=k (q1q2)/Dr^2
What is the energy of interaction equation used for?
To measure how much energy is required to separate two ions. E=k (q1q2)/ Dr
E<0 is attraction
If D of water is 80 and D of methanol is 33 how would the energy of interaction change if you made an aqueous solution with Mg ions and Br ions in methanol compared to water?
The energy of interaction would increase as you are dividing by a smaller number.
E=k (q1q2)
_______
Dr
What does it mean to say dipole interaction?
There is a partial charge. They can be polar and induced (polarizable)
Charged attraction
What is a Dispersion interaction?
Type of electrostatic interaction, also called Van Der Waals or hydrophobic interactions. Charged attraction. An example is stacking benzene rings or stacking nucleotides
Describe Hydrogen bonds.
Type of electrostatic interaction. A hydrogen atom is shared between two molecules. Example is nucleotide base pairing.
Describe hydrogen bonds at solid liquid and gas states?
In a solid phase hydrogen bonds are optimal . Liquid has sub optimal hydrogen bonds and gasses do not have hydrogen bonds.
Describe why Ice floats.
Ice is less dense than water due to the distance between hydrogen bonds. Density is how tightly packed molecules are and they are more tightly packed in water than ice.
Do hydrogen bonds use or release energy when they form?
Hydrogen bonds release energy when they are formed and use energy to break.
Difference between cohesion and adhesion?
Cohesion is attraction to self and adhesion is attraction to other. So water molecules attracted to more water and water attracted to other polar substances.
What happens to energy when noncovalent interactions break and form?
Breaking:use
Forming:release
What happens to energy when covalent bonds break and form?
Breaking:release
Forming:use
If pH is less than pKa are molecules protonated or deprotonated?
Protonated
If pH is greater than pKa are molecules protonated or deprotonated?
Deprotonated, less H ions floating around
What is the pKa of carboxyl on amino acids and the amine?
Carboxyl is about 2 and amine is around 9
If pH is less than pI what is the overall charge?
Positive charge
If pH is greater than pI what is overall charge?
Negative
If pH=pI what is the charge?
No net charge because pI is the pH where all molecules have overall charge of 0.
During Isoelectric Focusing when do proteins stop moving and how does this work?
Isoelectric focusing changes the pH as you move further down the gel so you are separating proteins by pI. Proteins stop moving when they are no longer charged, which means that pH=pI.
At a high pH (pH>pI) is the protein protonated or deprotonated and is it soluble or insoluble?
Deprotonated and soluble. Molecules are negatively charged and repel each other
At isoelectric point do proteins aggregate or repel and become soluble or insoluble?
Aggregate and precipitate out
if pH is less than pI are proteins protonated or not and soluble or insoluble?
They are protonated and soluble At low pH the protins are soluble because of repulsions due to their positive charges.
Where does the lowest solubility occur?
at the isoelectric point
What is an open system?
Energy can be exchanged between system and surroundings
What is a closed system?
Energy cannot leave the system
What type of metabolic reaction (ababolism/catabolism) has a higher rate of entropy?
Catabolic, large molecules are broken down into smaller ones releasing energy.
What is the Gibbs Free energy equation?
G=H-T^S
What does it mean if Enthalpy changes?
the system is not closed
What drives the sign of delta G?
TS
What does a negative G mean?
Free energy is released and the reaction is exergonic and favorable as well as spontaneous.
When Q=K what happens?
The reaction is at equillibrium
If Q
the reaction goes towards the products
If Q>K what happens?
the reaction goes to the left to reactants
