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Molec Biology > Test One Chapter Three > Flashcards

Test One Chapter Three Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

what is van der waals bond

A

depends on distance between interacting atoms, need multiple atoms in the two molecules

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2
Q

if atom loses electron it becomes

A

electropositive

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3
Q

ionic bonds form

A

salt bridges

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4
Q

if reaction is not spontaneous what is the sign of delta G

A

positive

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5
Q

H is usually what in the hydrogen bond

A

donor

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6
Q

on the scale what determines covalent

A

zero

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7
Q

why is ATP a good way to store and transfer energy in the cell

A

even though it takes energy to break ATP, hydration of the breakdown products of ATP more than makes up for the input of energy necessary to break the bond, resulting in an overall energetically favorable process

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8
Q

how does RNA differ from DNA

A

ribonucleotides, OH on 2 carbon, uracil

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9
Q

which has more different types of cellular functions proteins or nucleic acids

A

proteins

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10
Q

what is a nucleic acid built from

A

nitrogenous base, 5 carbon sugar (pentose), phosphate group

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11
Q

what is the equilibrium constant

A

Keq

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12
Q

what is a feature of enzymes

A

very specific to substrate and their activity is regulated

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13
Q

what is the van der waals radius

A

attractive and repulsive forces are equal

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14
Q

what is an ionic bond

A

one atom donates an electron to another atom, between metal and non metal

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15
Q

what is a nucleotide

A

base, pentose, phosphate

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16
Q

what does it mean that ATP is hydrolyzed

A

water breaks down ATP to ADP

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17
Q

which nucleotides are pyrimidines

A

C, T and U

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18
Q

what are some modifications of amino acids

A

methylation, phosphorylation (PO3-), acetylation (COCH3), glycosylation, hydroxylation (OH)

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19
Q

nucleic acids are synthesized using which enantiomer of the sugar

A

D form, think of D ribose

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20
Q

non polar has what type of charges

A

balanced

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21
Q

which nucleotides are purines

A

A and G

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22
Q

what is a transition state intermediate

A

it is the intermediate before the new molecule is formed which involves the reactants coming together and bonds are breaking and forming

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23
Q

how does the transition state intermediate relate to the free energy level of the reactants and the products

A

going from reactants to products occurs spontaneously and is now favorable

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24
Q

what is electronegativity

A

propensity of an atom within a molecule to attract electrons to itself

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25
Q

how does the enzyme affect the delta G of a reaction

A

delta G is not affected by the enzyme

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26
Q

what is an enantiomer

A

stereoisomers that are mirror images

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27
Q

what is a nucleoside

A

base and pentose

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28
Q

what is polar covalent

A

electrons shared between atoms but favor one pole of the two atoms

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29
Q

what does - delta G tell us about the reaction

A

not spontaneous and requires energy

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30
Q

what is an energy carrier in the cell

A

stored in chemical bonds, energy rich covalent bonds,

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31
Q

how many H bonds in G-C

A

three

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32
Q

what is hydrogen bonding

A

intermolecular force between two partial electrical charges of opposite polarity

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33
Q

what is an example of van der waals

A

antibodies, macromolecules contain surface that precisely fits the shape of molecule it binds to

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34
Q

proteins are synthesized using which enantiomer of amino acids

A

L form

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35
Q

the second law of thermodynamics determines what

A

the direction a reaction will move

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36
Q

what happens to the water in the hydrophobic bond

A

H2O attracted to each other causing unfavorable organization of H2O molecules

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37
Q

why is stereochemistry important in molecular interactions

A

helps determine structure and determines how that particular molecule will interact with other molecules

38
Q

structure determines

A

function

39
Q

how does an enzyme affect the energy of activation

A

lowers the activation of energy

40
Q

what is a chiral carbon

A

optically active, not imposable on mirror image, connected to four different atoms

41
Q

in hydrogen bonding, H bonds to

A

O, N , or F

42
Q

what are some modifications to RNA

A

loss of amino group, methylation to bases, methylation to pentose

43
Q

how does an enzyme work with reaction coupling

A

an enzyme can couple exergonic reactions with endergonic reactions to result in a coupled reaction that is exergonic overall

44
Q

what is the first law of thermodynamics

A

energy can never be created or destroyed, can either transfer or form to heat

45
Q

what determines strength in ionic bonds

A

salt concentration and hydrophobicity of environment

46
Q

on periodic table, where is electronegativity

A

going from left to right, down to up

47
Q

what happens to entropy in the hydrophobic bond

A

entropy decreases when water can form around the two separate non polar structures but when the aggregate towards each other the entropy increases for water

48
Q

what influences the rate of a reaction

A

enzyme stabilizes transition state, lower activation energy, substrates bind to enzymes in an orientation that favors the reaction, chemical groups in enzyme bind to metal ions or proteins that participate in reaction, relative concentration of both the products and reactants

49
Q

if the atomic radius decreases what happens to electronegativity

A

increases

50
Q

what is stereochemistry

A

spatial arrangement of atoms within a molecule

51
Q

polar molecules have what type of charges

A

unbalanced

52
Q

what makes RNA different than DNA

A

uracil, less stable, shorter, OH on C’2

53
Q

on the scale what determines ionic

A

> 1.67

54
Q

what is a stereoisomer

A

2 molecules that have the same chemical and structural formula but differ in the arrangement of their atoms in space

55
Q

are most reactions spontaneous

A

no

56
Q

Uracil replaces what in RNA

A

thymine

57
Q

if the Keq >1 then what about delta G

A

delta G is large and negative and the reaction goes to completion

58
Q

what is a chemical reaction

A

breakage of covalent bonds and the formation of new bonds, this creates reactants and products

59
Q

what is Gibbs free energy

A

energy that is available to do work

60
Q

how does the enzyme affect the overall stability of the coupled reaction

A

the enzyme makes the reaction exergonic and spontaneous, energy level of the product is lower than the reactant allowing the reaction to proceed forward

61
Q

how many h bonds in A-T

A

two

62
Q

what do the RNA modifications do

A

affect ability of RNA molecules to fold into a 3D shape and to interact with proteins

63
Q

what are some modifications to DNA

A

methylation

64
Q

what is a hydrophobic bond

A

strong tendency of H2O to exclude nonpolar groups, forcing nonpolar groups to aggregate to each other

65
Q

whats the strongest bond

A

covalent

66
Q

what happens during methylation of DNA

A

added to C, A, G and needed for DNA replication and protection from degredation

67
Q

if the Keq<1 then what about delta G

A

delta G is large and positive

68
Q

what is reaction coupling

A

an energetically favorable reaction is directly linked to an energetically unfavorable reaction

69
Q

what is equilibrium

A

when the reaction can move forward or reverse

70
Q

the strands of DNA are what and what direction

A

anti parallel, 5’ to 3’

71
Q

what is pi stacking

A

non covalent, overlap between the electrons in neighboring rings

72
Q

where do you see hydrogen bonding

A

proteins, DNA, alpha helices, beta sheets

73
Q

what is entropy

A

the extent of randomness or disorder in a system

74
Q

function of stereochemistry

A

determine structure, how interacts with other molecules

75
Q

what other types of bonds stabilize DNA double helix

A

hydrogen bond, pi stacking (non covalent), van der waals

76
Q

what is the second law of thermodynamics

A

all spontaneous processes take place with an increase in disorder of the system, entropy

77
Q

if atom gains electron it becomes

A

electronegative

78
Q

what are considered weak bonds

A

van der waals, hydrophobic, hydrogen

79
Q

why do you usually go from reactants to products

A

the energy difference between the products and transition state is greater than the reactants and transition state, this creates more products than reactants

80
Q

how does gibbs free energy reflect favorability or spontaneity of a reaction

A

free energy always decreases in spontaneous reactions that occur with a change in temperature or pressure, -G

81
Q

what type of bonds are required for nucleic acids to form

A

phosphodiester bond, O bonds with 5’ CH2 and 3’ carbon bind to O

82
Q

what is the advantage of weak bonds

A

greater distance between molecules and more easily broken

83
Q

what is the valence bond model

A

chemical bond forms when there is suitable overlap between electron clouds, aka molecular orbital model

84
Q

what is the energy of activation

A

the difference in free energy between the ground state of a reacting substance and the transition state

85
Q

whats in a polypeptide

A

amino group, alpha carbon with r chain, carboxyl group

86
Q

what does + delta G tell us about the reaction

A

reaction goes to completion

87
Q

on the scale what determines polar covalent

A

0 to < 1.67

88
Q

what is a covalent bond

A

2 atoms share a pair of electrons between nuclei, outer electron shells filled

89
Q

what do the modifications do to amino acids

A

control production of proteins from specific genes, distinguish self from non self

90
Q

which amino acids does not have an enantiomer and why

A

glycine because has two hydrogens as side chains from alpha carbons

91
Q

what is different in the RNA pentose than DNA

A

OH on C’2

92
Q

what are examples of energy carrier in the cell

A

ATP, NADH, NADPH, coenzymes, and enzymes

Molec Biology (3 decks)

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