Exam 1 Lectures 1-3 Flashcards
Properties of a covalent bond include:
Atoms are close together ie strong, short bonds because sharing electrons
properties of a non-covalent bond
Attractive forces ie do not not need to be close to one another. Weak and long bods. Includes ions
Covalent bonds make molecules: T/F?
True
What are the type of covalent bonds for:
- Proteins?
- Carbohydrates
- Lipids
- Nucleic acids
- Peptide
- Glycosidic
- Ester
- Phosphodiester
How is the strength of a covalent bond measured?
Measured by how much energy is needed to break apart. High energy needed bc of closeness
How is the strength of a non-covalent bond measured?
Measured by how much less energy is needed to break bond. Bc of how far apart they are, requires less energy.
What are the types of non-covalent interactions:
Charge-charge
Dipole
Hydrogen Bond
What are 2 examples of charge-charge bonds?
Ionic bonds and salt bridges
If F>0 what does that tell us about charge?
Positive number bc 2 pos charges = a pos number which means they are like charges and REPEL
What does F<0 tell us:
Negative number bc one is bigger than the other and 2 opposite charges ie ATTRACTIVE
In a vacuum we use __ law but in a biological environment, we use __?
Coulomb’s law and Relative permittivity (D)
What is D?
Dielectric constant accounts for “stuff” that prevents electrons from interacting with one another
What is the energy of interaction
Energy required to separate 2 ions
E<0 means:
Considering the attraction
What is a dipole interaction?
Deals with partial charges; similar to charge-charge interactions
Dipole interactions are highly dependent on what?
Distance
T/F: dipoles can be permanent (polar) or induced (polarizable)?
True
What exactly is a H bond?
Sharing of a H+
What is an example of H bond?
Nucleotide base pairing
Wha is the nature of interaction for Van der Waals?
Charge attraction
H20 is what type of interaction?
Non-covalent
What are characteristics of H20 as a solid?
Has optimal H bonds and bonds are long
What are characteristics of H20 in a liquid state
Suboptimal H bonds, back and forth motion of bonds (far and close)
What are the characteristics of H20 as a gas
No H bonds
Is ice less/more dense than liquid H20?
Less
What is specific heat capacity?
Amount of heat needed to change the temp of 1g of a given substance by +/- 1 degree Celsius
What is heat of vaporization defined as:
Amount of energy needed to change 1g of a given substance from liquid to gas
H bonds __ energy to break and ___ energy when they form
Use and release
What is cohesion?
Attraction to self
What is adhesion?
Attraction to other
What creates surface tension
Cohesion
What creates capillary action
Cohesion and adhesion working together
Charged/polar molecules are in H20 solvent?
Hydrophilic and dissolve
Nonpolar molecules are what in H20 solvent?
Hydrophobic and separate
Covalent bonds ___ energy when broken
Release
Covalent bonds __ energy to form
Use
Noncovalent interactions __ energy to break
Use
Noncovalent interactions __ energy when formed
Release
T/F: everything is reversible
True
HA <=> A- + H+
What is the donor?
What is the acceptor?
HA is the weak acid donor
A- is the conjugate base acceptor
A weak acid’s Ka is smaller/larger and why?
Smaller bc not likely to fall apart
A strong acid Ka is smaller/larger and why?
Larger bc falls apart completely (large numbers of conj base and H+)
Energy of interaction is smaller larger in a weak acid? Why?
Larger because 2 ions are more attractive to one another
Weak acid has smaller/larger pka?
Larger
Strong acid has smaller/larger pka? Why?
Smaller bc how attractive conj base is to H+
Energy of interaction in strong acid is smaller/larger
Smaller
B + H20 <=> BH+ + OH-
What is the acceptor?
What is the donor?
B is the weak base acceptor
BH+ is the conjugate acid donor
Strong base has smaller/larger Kb?
Larger
Strong base has smaller/larger pKb?
Smaller
Energy of interaction smaller/larger in strong base?
Larger
Weak base has smaller/larger Kb?
Smaller
Weak base has smaller/larger pKb?
Larger
Weak base has smaller/larger energy of interaction?
Smaller
Low pH means what about the H+
More (most) H+
What is the purpose of a buffer?
Weak acid base that help stabilize pH able to absorb change in H+ concentration
How dos gel electrophoresis work?
Direction of migration based on net charge of molecule
Wha is the isoelectric point (pI)
The pH where ALL molecules of a given species in sol’n have an overall average charge of 0
Ph is less than pI
Molecule has a positive charge
pH>pI
Molecule has negative charge
pH=pI
Molecule has no net charge
What happens if there are 3 pKas and trying to find pI?
All we care about are the 2 pKas that get us to our species isoelectric point (2 pKas for average)
Protein stops moving in isoelectric focusing when…
pH = pI (separating based on pI of protein)
Are proteins soluble when pH=pI
No
What is the 1st law of thermodynamics
Energy is neither created or destroyed in a CLOSED sys
Can you convert btwn energy (PE & KE) without violating the 1st rule of thermodynamics?
Yes
What is PE?
Position, potential to do work.
What is KE?
Motion, performing work
What is an example of PE?
Chemical energy- PE within chemical bonds. Electrons with an atom (push/pull of e-s and protons)
What is an example of KE?
The atom itself
How does energy function in a closed system?
Energy cannot leave in or out
What is an example of a closed system?
The universe
How does energy function in an open system?
Energy exchanged btwn system and surroundings (can go and come as it pleases to surroundings) can add and subtract
What is an example of an open sys
A cell. The universe is the surroundings
What is the 2nd law of TD?
Disorder is increasing
What is disorder seen as in TD?
Entrophy seen as heat bc we are in pieces/mobile which generates heat
Which is more disordered: anabolic or catabolic?
Anabolic
Define anabolic
Synthesis. Monomers into polymers; assembly of many pieces into 1 piece
Define catabolic
Breaking polymers into monomers
How do we measure energy in TD?
Gibbs free
What is: Delta G Delta H T Delta S
Delta G = change in energy
Delta H = change in total energy = enthalpy in sys
T = kelvin (+273)
Delta S = entropy change in disorder
What drives the sign of delta G?
TdeltaS
-deltaH and +deltaS =
Spontaneous at all temps
+deltaH and -deltaS =
Non spontaneous at all temps
+deltaH and +deltaS =
Spontaneous only at high temps
-deltaH and -deltaS =
Spontaneous only at low temps
When deltaG is negative:
Free energy released; EXERGONIC favorable rxn (to products)
When deltaG is positive:
Free energy required; ENDERGONIC rxn unfavorable (reverse rxn to reactants)
When do you need high disorder?
To do work; energy is added to the sys thus incr deltaH and incr deltaS
When do you need low disorder?
For disorder to ‘go away’ energy is releases from the open sys
What is important about a state function and examples:
We only care about where we end ie deltaG, deltaH, and deltaS
Most energetic state is _ state and what does this mean?
Transition state and very unstable
What lowers the activation energy and how?
Enzymes by stabilizing the transition state
What are the 4 ways to stabilize the transition state?
- Substrate orientation
- Straining substrate bonds
- Favorable microenvironment
- Covalent bonding with substrate
Protein folding: spon or non spon?
Spontaneous!
Net effect is equal to:
Sum all sources of energy
T/F: reactions exist in a vacuum?
FALSE. Reactions do no exist in a vacuum thus non-equilibrium concentrations
What is the equilibrium constant?
“Q” = products/reactants
Q less than K
Rxn towards products (forward to the right)
Q>K =
Rxn towards reactants (to the left; reverse)
Movement of e-s and concentration gradients across a barrier account for influences of process happening in a __
Cell
What is biology standard state concentration?
1M except H+ (=10^-7M)
How do we drive and unfavorable reaction?
- Use up the products!
2. Couple it to a favorable exergonic rxn ie ATP hydrolysis
T/F: reaction and deltaG values can be summed
True
