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Biochemistry > Molecular Properties Lectures 1 & 2 Ford > Flashcards

Molecular Properties Lectures 1 & 2 Ford Flashcards

1
Q

Briefly describe the differences between covalent and noncovalent bonds

A

covalent bonds- strong, short, and share electrons

non covalent- weak, long, and attraction only

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2
Q

Describe the types of bonds between

  1. carbohydrates
  2. lipids
  3. proteins
  4. nucleic acids
A
  1. glycosidic
  2. ester
  3. peptide
  4. phosphodiester
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3
Q

Describe electrostatic interactions

A

interaction between 2 charged ions

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4
Q

Define a dipole

A

molecule has a “partial charge”; can be permanent or induced

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5
Q

What are some examples of electrostatic interactions?

A

stacking of benzene rings, stacking of nucleotides, nucleotide base pairing

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6
Q

If the force between two ions is positive, what does that mean? If negative?

A

positive=repulsive

negative=attractive

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7
Q

Describe covalent bonds in terms of

  1. nature of interaction
  2. average bond distances
  3. average bond energies
A
  1. share an electron pair 2. 1 A

3. 355 kj/mol

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8
Q

Describe charge and or dipole interactions in terms of

  1. nature of interaction
  2. average bond distances
  3. average bond energies
A
  1. charge attraction
  2. 3 A
  3. 5.86 kJ/mol
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9
Q

Describe van der waals interactions in terms of

  1. nature of interaction
  2. average bond distances
  3. average bond energies
A
  1. charge attraction
  2. varies by atom sized
  3. 2-4 kj/mol
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10
Q

Describe the H bonds that are present in solids liquids and gasses

A
  1. solids have optimal H bonds; they perfect
  2. liquids have suboptimal H bonds; they are trying to be the best that they can be but are not quite there (me)
  3. gasses have no H bonds because they are too hyperactive and are not able to even interact with each other. they are too self absorbed to stop and say hello to their neighbors
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11
Q

Describe ice versus water in terms of hydrogen bonding

A

Water is more dense than the ice and has shorter distances between the molecules that does not allow for h bonding

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12
Q

Define specific heat capacity

A

the amount of heat needed to change the temperature of a 1g of a given substance by +/- 1 C

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13
Q

Define heat of vaporization

A

the amount of energy needed to change 1 g of a given substance from a liquid to a gas

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14
Q

Define cohesion

A

attraction of water molecules to each other

create surface tension

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15
Q

Define adhesion

A

attraction of water molecules to other polar substances

cohesion and adhesion make capillary action

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16
Q

Describe what a charged/polar molecule does in solution

A

It is hydrophilic and dissolves

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17
Q

Describe what non polar molecules do in solution

A

they are hydrophobic and separate

18
Q

What is the relationship between Ka and a strong or weak acid?

A

A strong acid has a larger Ka and a weak acid has a smaller Ka

19
Q

What is the relationship between pka and the strength of an acid

A

strong acids have a smaller pka and weak acids have a larger pka

20
Q

What is the relationship between the energy of interaction and the strength of an acid?

A

Strong acids have smaller energies of interactions and weak acids have a larger energy

21
Q

What is the relationship between Kb and the strength of a base?

A

The stronger the base, the larger the Kb and vice versa

22
Q

What is the relationship between pkb and the strength of the base?

A

The stronger the base, the smaller the pkb and vice versa

23
Q

What is the relationship between the energy of interaction and the strength of the bases?

A

The stronger the base, the larger the energy of interaction and vice versa

24
Q

Define pH in terms of H+

A

pH=-log[H+]

25
Q

Define pkw

A

pH+pOH

26
Q

Define buffers

A

weak acids of bases that can stabilize pH

27
Q

What is the Hendersen Hasselbalch derivation?

A

pH=pKa + log ([A-]/[HA])

OR

[A-]/[HA]=10^pH-pKa

28
Q

If the pH

A

The molecule is protonated since

[HA]>[A-]

29
Q

If the pH>pKa, what does it mean for the molecule itself?

A

That the molecule is deprotonated since [Ha]

30
Q

What happens if the pH and pKa are equal?

A

Then the molecule is just as likely to be protonated as it is deprotonated

31
Q

Describe gel electrophoresis

A

the direction of migration based on the net charge of molecule

32
Q

Define isoelectric point and give the equation and the relationships between the pH and the pI

A

isoelectric point- the pH where aLL molecules of a given species in a solution have an overall charge of 0

pI=(pKa(+1) + pKa(-1)/2)

if pH< pI then the molecule has a positive charge
if pH>pI then the molecule has a negative charge
if they are equal, then there is no net charge

33
Q

What is the first law of thermodynamics?

A

Energy is neither created nor destroyed in a closed system (energy cannot leave the system)

34
Q

Define kinetic energy

A

motion

35
Q

Define potential energy

A

position; potential to do work- the potential energy within chemical bonds

36
Q

What is the second order of thermodynamics?

A

Disorder is increasing… catabolic reactions would be an increase in disorder because there are more individual molecules

37
Q

Describe Gibbs Free Energy Equation

A

deltaG=deltaH-TdeltaS

delta G is the change in the available/usable energy

delta H is the change in the totally energy (enthalpy)

deltaS is the change in disorder

38
Q

Define a state function and what is an example of a state function>

A

a state functions value depends only on the initial and final values, not the pathway to get there

delta G, S and H are state functions

39
Q

What happens if the delta H is negative? positive? zero?

A
  1. negative: energy is released from the system
  2. positive: energy is added to the system
  3. zero: closed system
40
Q

What happens if the delta S is negative? positive? zero?

A

Negative: disorder decreases
Positive: disorder increases
Zero: no net change

41
Q

What happens if the delta G is negative? positive? or zero?

A

negative: free energy is released; exergonic reaction; favorable reaction; spontaneous reaction
positive: free energy is required; endergonic reaction; unfavorable reaction; driven reaction
zero: equilibrium

Biochemistry (12 decks)

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