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Biochemistry > Exam 1 Lectures 1-3 > Flashcards

Exam 1 Lectures 1-3 Flashcards

1
Q

Properties of a covalent bond include:

A

Atoms are close together ie strong, short bonds because sharing electrons

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2
Q

properties of a non-covalent bond

A

Attractive forces ie do not not need to be close to one another. Weak and long bods. Includes ions

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3
Q

Covalent bonds make molecules: T/F?

A

True

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4
Q

What are the type of covalent bonds for:

  1. Proteins?
  2. Carbohydrates
  3. Lipids
  4. Nucleic acids
A
  1. Peptide
  2. Glycosidic
  3. Ester
  4. Phosphodiester
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5
Q

How is the strength of a covalent bond measured?

A

Measured by how much energy is needed to break apart. High energy needed bc of closeness

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6
Q

How is the strength of a non-covalent bond measured?

A

Measured by how much less energy is needed to break bond. Bc of how far apart they are, requires less energy.

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7
Q

What are the types of non-covalent interactions:

A

Charge-charge
Dipole
Hydrogen Bond

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8
Q

What are 2 examples of charge-charge bonds?

A

Ionic bonds and salt bridges

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9
Q

If F>0 what does that tell us about charge?

A

Positive number bc 2 pos charges = a pos number which means they are like charges and REPEL

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10
Q

What does F<0 tell us:

A

Negative number bc one is bigger than the other and 2 opposite charges ie ATTRACTIVE

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11
Q

In a vacuum we use __ law but in a biological environment, we use __?

A

Coulomb’s law and Relative permittivity (D)

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12
Q

What is D?

A

Dielectric constant accounts for “stuff” that prevents electrons from interacting with one another

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13
Q

What is the energy of interaction

A

Energy required to separate 2 ions

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14
Q

E<0 means:

A

Considering the attraction

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15
Q

What is a dipole interaction?

A

Deals with partial charges; similar to charge-charge interactions

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16
Q

Dipole interactions are highly dependent on what?

A

Distance

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17
Q

T/F: dipoles can be permanent (polar) or induced (polarizable)?

A

True

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18
Q

What exactly is a H bond?

A

Sharing of a H+

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19
Q

What is an example of H bond?

A

Nucleotide base pairing

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20
Q

Wha is the nature of interaction for Van der Waals?

A

Charge attraction

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21
Q

H20 is what type of interaction?

A

Non-covalent

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22
Q

What are characteristics of H20 as a solid?

A

Has optimal H bonds and bonds are long

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23
Q

What are characteristics of H20 in a liquid state

A

Suboptimal H bonds, back and forth motion of bonds (far and close)

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24
Q

What are the characteristics of H20 as a gas

A

No H bonds

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25
Q

Is ice less/more dense than liquid H20?

A

Less

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26
Q

What is specific heat capacity?

A

Amount of heat needed to change the temp of 1g of a given substance by +/- 1 degree Celsius

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27
Q

What is heat of vaporization defined as:

A

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

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28
Q

H bonds __ energy to break and ___ energy when they form

A

Use and release

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29
Q

What is cohesion?

A

Attraction to self

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30
Q

What is adhesion?

A

Attraction to other

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31
Q

What creates surface tension

A

Cohesion

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32
Q

What creates capillary action

A

Cohesion and adhesion working together

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33
Q

Charged/polar molecules are in H20 solvent?

A

Hydrophilic and dissolve

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34
Q

Nonpolar molecules are what in H20 solvent?

A

Hydrophobic and separate

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35
Q

Covalent bonds ___ energy when broken

A

Release

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36
Q

Covalent bonds __ energy to form

A

Use

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37
Q

Noncovalent interactions __ energy to break

A

Use

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38
Q

Noncovalent interactions __ energy when formed

A

Release

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39
Q

T/F: everything is reversible

A

True

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40
Q

HA <=> A- + H+

What is the donor?
What is the acceptor?

A

HA is the weak acid donor

A- is the conjugate base acceptor

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41
Q

A weak acid’s Ka is smaller/larger and why?

A

Smaller bc not likely to fall apart

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42
Q

A strong acid Ka is smaller/larger and why?

A

Larger bc falls apart completely (large numbers of conj base and H+)

43
Q

Energy of interaction is smaller larger in a weak acid? Why?

A

Larger because 2 ions are more attractive to one another

44
Q

Weak acid has smaller/larger pka?

A

Larger

45
Q

Strong acid has smaller/larger pka? Why?

A

Smaller bc how attractive conj base is to H+

46
Q

Energy of interaction in strong acid is smaller/larger

A

Smaller

47
Q

B + H20 <=> BH+ + OH-

What is the acceptor?
What is the donor?

A

B is the weak base acceptor

BH+ is the conjugate acid donor

48
Q

Strong base has smaller/larger Kb?

A

Larger

49
Q

Strong base has smaller/larger pKb?

A

Smaller

50
Q

Energy of interaction smaller/larger in strong base?

A

Larger

51
Q

Weak base has smaller/larger Kb?

A

Smaller

52
Q

Weak base has smaller/larger pKb?

A

Larger

53
Q

Weak base has smaller/larger energy of interaction?

A

Smaller

54
Q

Low pH means what about the H+

A

More (most) H+

55
Q

What is the purpose of a buffer?

A

Weak acid base that help stabilize pH able to absorb change in H+ concentration

56
Q

How dos gel electrophoresis work?

A

Direction of migration based on net charge of molecule

57
Q

Wha is the isoelectric point (pI)

A

The pH where ALL molecules of a given species in sol’n have an overall average charge of 0

58
Q

Ph is less than pI

A

Molecule has a positive charge

59
Q

pH>pI

A

Molecule has negative charge

60
Q

pH=pI

A

Molecule has no net charge

61
Q

What happens if there are 3 pKas and trying to find pI?

A

All we care about are the 2 pKas that get us to our species isoelectric point (2 pKas for average)

62
Q

Protein stops moving in isoelectric focusing when…

A

pH = pI (separating based on pI of protein)

63
Q

Are proteins soluble when pH=pI

A

No

64
Q

What is the 1st law of thermodynamics

A

Energy is neither created or destroyed in a CLOSED sys

65
Q

Can you convert btwn energy (PE & KE) without violating the 1st rule of thermodynamics?

A

Yes

66
Q

What is PE?

A

Position, potential to do work.

67
Q

What is KE?

A

Motion, performing work

68
Q

What is an example of PE?

A

Chemical energy- PE within chemical bonds. Electrons with an atom (push/pull of e-s and protons)

69
Q

What is an example of KE?

A

The atom itself

70
Q

How does energy function in a closed system?

A

Energy cannot leave in or out

71
Q

What is an example of a closed system?

A

The universe

72
Q

How does energy function in an open system?

A

Energy exchanged btwn system and surroundings (can go and come as it pleases to surroundings) can add and subtract

73
Q

What is an example of an open sys

A

A cell. The universe is the surroundings

74
Q

What is the 2nd law of TD?

A

Disorder is increasing

75
Q

What is disorder seen as in TD?

A

Entrophy seen as heat bc we are in pieces/mobile which generates heat

76
Q

Which is more disordered: anabolic or catabolic?

A

Anabolic

77
Q

Define anabolic

A

Synthesis. Monomers into polymers; assembly of many pieces into 1 piece

78
Q

Define catabolic

A

Breaking polymers into monomers

79
Q

How do we measure energy in TD?

A

Gibbs free

80
Q 
What is:
Delta G
Delta H
T 
Delta S
A

Delta G = change in energy
Delta H = change in total energy = enthalpy in sys
T = kelvin (+273)
Delta S = entropy change in disorder

81
Q

What drives the sign of delta G?

A

TdeltaS

82
Q

-deltaH and +deltaS =

A

Spontaneous at all temps

83
Q

+deltaH and -deltaS =

A

Non spontaneous at all temps

84
Q

+deltaH and +deltaS =

A

Spontaneous only at high temps

85
Q

-deltaH and -deltaS =

A

Spontaneous only at low temps

86
Q

When deltaG is negative:

A

Free energy released; EXERGONIC favorable rxn (to products)

87
Q

When deltaG is positive:

A

Free energy required; ENDERGONIC rxn unfavorable (reverse rxn to reactants)

88
Q

When do you need high disorder?

A

To do work; energy is added to the sys thus incr deltaH and incr deltaS

89
Q

When do you need low disorder?

A

For disorder to ‘go away’ energy is releases from the open sys

90
Q

What is important about a state function and examples:

A

We only care about where we end ie deltaG, deltaH, and deltaS

91
Q

Most energetic state is _ state and what does this mean?

A

Transition state and very unstable

92
Q

What lowers the activation energy and how?

A

Enzymes by stabilizing the transition state

93
Q

What are the 4 ways to stabilize the transition state?

A
  1. Substrate orientation
  2. Straining substrate bonds
  3. Favorable microenvironment
  4. Covalent bonding with substrate
94
Q

Protein folding: spon or non spon?

A

Spontaneous!

95
Q

Net effect is equal to:

A

Sum all sources of energy

96
Q

T/F: reactions exist in a vacuum?

A

FALSE. Reactions do no exist in a vacuum thus non-equilibrium concentrations

97
Q

What is the equilibrium constant?

A

“Q” = products/reactants

98
Q

Q less than K

A

Rxn towards products (forward to the right)

99
Q

Q>K =

A

Rxn towards reactants (to the left; reverse)

100
Q

Movement of e-s and concentration gradients across a barrier account for influences of process happening in a __

A

Cell

101
Q

What is biology standard state concentration?

A

1M except H+ (=10^-7M)

102
Q

How do we drive and unfavorable reaction?

A
  1. Use up the products!

2. Couple it to a favorable exergonic rxn ie ATP hydrolysis

103
Q

T/F: reaction and deltaG values can be summed

A

True

Biochemistry (32 decks)

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