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Biochem midterm exam 1 > Study guide 1 > Flashcards

Study guide 1 Flashcards

1
Q

What is thermodynamics (TD)?

A

the study of energy and its effects on matter and explains exchanges between heat, energy, and work.

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2
Q

Heat

A

a form of thermal energy transferred to the system.

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3
Q

Energy

A

The capacity to do work for transfer of heat

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4
Q

Work

A

Energy given to the environment

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5
Q

What does TD indicate?

A

the direction of the process/reaction(spontaneity)

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6
Q

What are the 3 types of system

A

isolated, closed, and open

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7
Q

What is an isolated system

A

no exchange of matter or energy with surrounding

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8
Q

Closed system

A

exchange of only energy, but not matter (temperature changes)

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9
Q

Open system

A

exchange of both matters and energy

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10
Q

TD 1st law

A

energy is conserved and cannot be created or destroyed

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11
Q

TD 2nd law

A

Spontaneous processes are characterized by conversion of order to disorder.

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12
Q

Weak acids are-

A

only partially ionized in aqueous solutions

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13
Q

If ∆H < 0, (is negative

A

heat is given off and is exothermic and enthalpically favored

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14
Q

what is a conjugate acid of H2PO4-

A

H3PO4

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15
Q

If ∆H > 0, (is postive)

A

heat is absorbed, endothermic and enthalpically opposed

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16
Q

internal energy (U

A

potential energy

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17
Q

Enthalpy (H)

A

total heat content of a system

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18
Q

Enthalpy change

A

heat absorbed in a constant P

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19
Q

If ∆S > 0 (is positive)

A

disorder increases entropically favored)

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20
Q

If ∆S < 0

A

disorder decreases (entropically opposed)

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21
Q

If ∆G > 0: postive

A

nonspontaneous (endergonic)

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22
Q

An endergonic with a —— ∆H and a —- ∆S can be changed into exergonic reaction by decreasing the temperature

A

negative, negative

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23
Q

If ∆G < 0

A

spontaneous (exergonic)

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24
Q

If q > 0

A

system absorbs heat from surroundings.

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25
Q

A spontaneous process

A

occurs without the addtion of free energy, is a negative, exergonic

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26
Q

Free energy is

A

additive

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27
Q

∆G rxn

A

products - reactiants

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28
Q

Spontaneous reaction equation

A

∆G = ∆H - T∆S ≤ 0

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29
Q

Molecules such as methanol and ethanol are very soluble in water because

A

they contain O-H groups that can form multiple H-bonds with water

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30
Q

If q < 0

A

system gives off heat (exothermic)

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31
Q

If w > 0, positive

A

system does work on surroundings

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32
Q

if w < 0 (negative)

A

surroundings do work on system

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33
Q

An endergonic with a —— ∆H and a —- ∆S can be changed into exergonic reaction by increase the temperature

A

postive, postive

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34
Q

negative ∆H and a postive ∆S =

A

negative ∆G, exothermic, enthalpically favored and entropically favored, spontaneous (exergonic)

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35
Q

postive ∆H and a negative ∆S

A

enthalpically and entropically opposed, non-spontaneous

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36
Q

Ionic interaction bond strength

A

86

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37
Q

Keq can be determined from the change in standard free energy using the equation

A

Keq = -∆Ho
/RT

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38
Q

van’t Hoff plot

A

determines ∆H and ∆S using ∆G o & Keq

39
Q

Slope

A

-∆Ho/R

40
Q

Y intercept

A

∆So/R

41
Q

Hydrophiles

A

polar and ionic

42
Q

Hydrophobes

A

non polar , not dipole

43
Q

Hydrophobic interactions between nonpolar molecules

A

require the prescene of surrounding water molecules

44
Q

Hydrogen bond, bond strength

A

20

45
Q

dipole diple interaction bond strength

A

9.3

46
Q

covalent bond examples

A

o-h-460
c-h,-414
c-c -348

47
Q

Ice

A

all 4 H bonds are satisfied, less dense, open structure

48
Q

Linker DNA length

A

8-114 bp

49
Q

O is electronegative, true or false

A

true

50
Q

structure of water

A

tetrahedron- sp3 hybridization with 2 lone electron pairs

51
Q

water is

A

polarized with a dipole moment

52
Q

How many of liquid ‘s H-bonds are satisfied

A

about 85%

53
Q

strength of H-bond is dependent on

A

orientation

54
Q

high dielectric constant

A

78-water
32.6-methanol
1.9-hexame

55
Q

DNA sequencing using the Sanger method requires

A

template, primer, DNA polymerase, dNTPs, ddNTPs

56
Q

Amphiphiles

A

Hydrophilic heads and hydrophobic tails and can form micelles or bilayers

57
Q

What are colligative propertties

A

properties that depend on # of solute particles
decrease freezing point.
raise boiling point.
lower vapor pressure
causes osmotic pressure.

58
Q

Which Topo requires ATP hydrolysis for energy?

A

Topo II

59
Q

non covalent interactions

A

-atoms are not covalently bonded to each other
-can be either attractive or repulsive
-arise from interaction between transient or stable charges on atoms
-influence the structure of biological macromolecules

60
Q

acid

A

anything capable of donating proton

61
Q

base

A

anything capable of accepting proton

62
Q

pH=

A
  • log10[H+ ]
63
Q

What does K -acidd disassociatio constant indicate

A

acid strength

64
Q

if K is large, pk is

A

small and vice versa

65
Q

Henderson-Hasselbalch equation:

A

pH = pK + log10([A-] / [HA]

66
Q

Henderson-Hasselbalch equation can determine

A

pH of solutiion if K and A and HA is known

67
Q

N-glycosidoc bonds between

A

N1 (pyrimidines) or N9(purines) and C2 of deoxyribose

68
Q

Phosphodiester bond between

A

5’ and 3’

69
Q

Base Pairing of DNA

A

T with A – 2-H bonds
C with G—3 H-bonds
A with U —2 H-bonds

70
Q

The sugar pucker is — in the – form

A

C2-endo; B-DNA
C3 endo; A-DNA

71
Q

Knowledge about the tautomeric forms of the base of nucleic acids is needed

A

to understand H-bonding between complementary bases

72
Q

B-DNA

A

Major: wide and deep
Minor: narrow and deep
C2-endo

73
Q

z-dna

A

major: flat
minor: narrow and deep
C2 endo for pyrimidines

73
Q

A-DNA

A

Major: narrow and deep
Minor: wide and shallow
C3 endo

74
Q

The pH of cofee is 5.6. The pH of grapefruitjuice is 2.6. That means the proton concentration in coffee is

A

a thousand times lower than grapefruit juice

75
Q

The polarity of the O-H bond is caused by the — of oxygen relative to that of hydrogen

A

higher electronegativity

76
Q

Due to constraints on its sugar pucker, when RNA forms a double helical structure its conformation is

A

A-form

77
Q

Nucleosome

A

1st level of packing
packing ratio: 6
winding of DNA around a protein core

78
Q

30nm Fiver (chromatin fiber)

A

2nd level of packing)
coiling of beeds in a helical structure
packing ratio–40

79
Q

300-700 nm fiber and chromosome -the final packaging

A

paking ratio 1000= interphase
10000- mitosis

80
Q

Hyperchromic effect/shift

A

the absorbance of denatured DNA is 30-40%

81
Q

Tm depends on 4 factors

A

GC content
salt concentration
sequence length
# gaps

81
Q

Gel electrophoresis`

A

separating DNA by size

82
Q

steps to PCR

A

denaturation–annealing– elongation

83
Q

PCR

A

amplifies specific regions of dna

84
Q

Sanger sequencing

A

limited incorporation of ddNTP results in a series of DNA fragments in various sizes

85
Q

Molecular cloning

A

constructs a recombinant DNA molecule to generate a population of identical DNA molecules

86
Q

What is packing ratio

A

length of dna

87
Q

Histones does what with DNA

A

they wrap around DNA

88
Q

Basic protons

A

have an affintiy for DNA

89
Q

Core DNA has how many base pairs

A

146

90
Q

What are some common features for cloning vector for transformation

A

Mutiple cloning site (polylinker
origin of replication
selection marker

91
Q

What is the major grooves of dsRNA for

A

hydrogen bonding with external groups

Biochem midterm exam 1 (10 decks)

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