Rowland Flashcards
Which macromolecules are soluble in water?
DNA, RNA always.
Carbohydrates and protein: yes/sometimes
Explain Hydrogen Bonding
Hydrogen bonds are formed between a proton (H atom) covalently bonded to an electronegative atom and a second electronegative atom that serves as the hydrogen bond acceptor.
What is a property of a biomolecule?
- have a restricted set of conditions at which they can work (temp, pH)
- altered by our metabolism (we can harvest energy to do this, or we harvest energy from them as we alter them)
- source components of biomolecules from the environment and/or we can produce our self.
What difference in bond polarity is need for a pond to be non-polar, polar covalent or ionic?
non-polar: 0-0.5
polar covalent: 0.5-1.7
ionic: >1.7
What is a covalent bond?
A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms; usually between to non-metals.
What happens when two atoms of unequal
electronegativity are covalently bonded to one another?
The atom that is more electronegative will draw the electrons closer to itself, creating a partial negative dipole at that end and a partial positive dipole at the atom with less electronegativity.
What are the major determinants of solubility in water?
Charge, polarity, and the ability to form
hydrogen bonds
What are the backbones of biomolecules made of and how are they bonded?
biomolecules have backbones that are
covalently bonded, and they are carbon-based backbones
Draw the structure of an amino acid
Amino group Carboxy Group R-group Hydrogen carbon center
What is the difference between intra and inter?
Intra: within one molecule
Inter: between two different molecules
When we cook an egg the proteins denature but do not degrade. Why?
Because the weak forces are broken but not the covalent bonds
Explain Van der Waals contact distance
The optimal distance between two atoms for the structural stability
The distance at which electrons interact optimally
How does water operate as a solvent?
Water is heavily hydrogen bonded to itself. The water molecules make and break these bonds repeatedly, with a half-life for each bond of about 10 psec. This is a highly thermodynamically favorable situation because it is chaotic, with many favorable bonds. Water soluble molecules make multiple favorable hydrogen bonds with water due to their own electronegative atoms.
What bond holds base pairs together?
Hydrogen bonds
What type of bond drives the secondary structure formation in proteins and carbohydrates?
Hydrogen bonds
What is the hydrophobic effect?
The hydrophobic effect is the observed tendency of nonpolar substances to cluster in aqueous solution and exclude water molecules.
What does the disparity in bond strength mean for biology?
- Some bonds are much stronger than others
- Some bonds need to stay intact under stress
- Some bonds are made to be broken
- Some interactions are reversible
- Some states are more energetically favorable than others.
Van der Waals forces, hydrogen bonds, and ionic bonds are all what type of forces?
electrostatic forces
How do electrostatic forces occur?
electrostatic forces occur when two particles of opposite charge are attracted to or repelled by one other
When we cook an egg the proteins denature but do not degrade. Why?
As the weak bonds are broken at cooking temperatures but the strong covalent bonds need more energy to break their bonds.
What is the strength of Van der Waals forces dependant on?
Strength depends on the relative size of the atoms or molecules and the relative distance between them. The greater the area, the stronger the interaction.
What is the van der Waals contact distance?
The optimal distance between two atoms for structural stability
How are hydrogen bonds formed?
Hydrogen bonds are formed between a proton (H atom) covalently bonded to an electronegative atom and a second electronegative atom that serves as the hydrogen bond acceptor.
How do you tell which is the donor and acceptor in a hydrogen bond?
The donor is the one with the hydrogen
The donor is the one that isn’t bonded to the hydrogen
Does water have a dipole? if so how?
why is water shaped like a V?
Water has a dipole (different charge on each end).
This is because Oxygen is electronegative. It takes electrons from the covalently bonded Hydrogens, leaving partial charges on the two ends of the molecule.
It is shaped like a “V” because of the lone pairs on the oxygen.
How does water operate as a solvent?
Water is heavily hydrogen bonded to itself. The water molecules make and break these bonds repeatedly. This is a highly thermodynamically favorable situation because it is chaotic, with many favorable bonds. Water soluble molecules make multiple favorable hydrogen bonds with water due to their own electronegative atoms.
Water interacts electrostatically with charged solutes (and with charged and polar biomolecules)
Water hydrates charged molecules, replacing solute-solute interactions with solute-water interactions. This reduces the solute tendency to self-associate.
This separation of the solute into individual molecules increases the entropy of the system and thus is energetically more favorable for the system.
What is the hydrophobic effect?
The observed tendency of non-polar substances to clump together in aqueous solution and exclude water molecules
Why does the Hydrophobic effect occur?
- Hydrophobic molecules in water interact unfavorably with water. This may happen via one of two mechanisms:
a) short-range ordering of water around the hydrophobic molecule
b) reduction of the number of favorable hydrogen bonds. - Ordered water (or water with a reduced # of hydrogen bonds) is highly energetically unfavorable.
- It is more energetically favorable for a biological system if the hydrophobic groups cluster together, leaving the water to be disordered and maximize the hydrogen bonding.
How are the phosphate groups removed from ATP?
Via nucleophilic attack
what is the difference between information rich and information poor molecule?
information rich: - negative entropy - non-chaotic information poor: - positive entropy - chaotic - low free energy
Why do biological molecules have high Gibbs free energy?
They take energy to build
They can be broken down to yield electrons
Will a negative or positive Gibbs free energy (delta G) occur spontaneously?
Negative delta G
How do you make a non-spontaeous reaction spontaneous?
By coupling it with a spontaneous reaction with a larger negative delta G
Define entropy?
give an example
chaos and randomness of a system e.g. break down of polymers into monomers or breakdown of crystalline structures into individual components
Define enthalpy?
the total heat content of a system at constant pressure and volume
what is the formula for Gibbs free energy?
delta G = delta H - T delta S
What is the first law of thermodynamics?
energy can not be created nor destroyed, only transferred from one form to another. Energy in the universe remains constant
what is the second law of thermodynamics?
in all natural processes the entropy of the universe increases.
Define Gibbs free energy?
the maximum amount of energy available from a reaction or system to do work under conditions of constant pressure and temperature
“available energy”
What does entropy show?
- the amount of flexion and rotation around bonds contained in the molecules that are in the system (reactants and products),
- the number of atoms or molecules in a system (a large number of small molecules is more entropic than a small number of large molecules) and
- the distance these things are from one another (molecules spread out over a large area is more entropic than the same number of molecules concentrated in a small area).
which part of ATP is used for energy?
the phosphate group
Why does ATP breakage give energy to systems?
because the phosphate group that is broken off joins with water, therefore energy is released.
how does ATP breakage give energy to systems?
- mechanical work: ATP phosphorylates motor proteins
- transport work: ATP phosphorylates transport proteins
- chemical work: ATP phosphorylates key reactants
Phosphoryl group transfer is a common mechanism of ATP energy donation. what are the 2 steps of this process?
- dephosphorylation of the ATP and the simultaneous phosphorylation of glutamate (group transfer)
- A substitution reaction where phosphate is a good leaving group
