1.1 - Physical and Chemical Foundations Flashcards
1
Q
what is the medium for all biochemical reactions?
A
aqueous solution/water
2
Q
what is built from elements and functional groups?
A
biomolecules
3
Q
types of biomolecules
A
amino acids, nucleotides, simple sugars, fatty acids
4
Q
what is built from biomolecules?
A
macromolecules
5
Q
types of macromolecules
A
proteins, DNA/RNA, carbs
6
Q
what pathways do macromolecules feed into?
A
metabolic pathways
7
Q
metabolic pathways
A
glycolysis, citrate cycle, beta-oxidation, urea cycle
8
Q
what do metabolic pathways function within?
A
cells
9
Q
what makes up cells
A
cell wall, plasma membrane, organelles
10
Q
what do cells make up
A
organisms
11
Q
where do organisms interact
A
ecosystems
12
Q
types of ecosystems
A
rivers, islands, forests, deserts
13
Q
what are the most abundant elements of the human body
A
carbon, nitrogen, oxygen, hydrogen
14
Q
elements that are still essential to life but in very small amounts ; usually specific to the function of a protein
example: Fe iron is essential to the function of hemoglobin
A
trace elements
15
Q
elemental components of metabolism
A
phosphorus, potassium, sulfur
16
Q
elemental components required for signaling
A
calcium, phosphorus, potassium, sulfur, chlorine, sodium
17
Q
what determines the personality of an organic compound
A
functional groups
18
Q
groups responsible for the chemical properties of biomolecules, determines behavior based on the combination and positioning of these functional groups within a protein
A
functional groups
19
Q
hydrocarbon skeletons with Hydrogens replaced by functional groups
A
molecules
20
Q
what do amino acids build
A
proteins
21
Q
what do nucleotides build
A
DNA/RNA
22
Q
what do simple sugars build
A
nucleotides and polysaccharides
23
Q
what do fatty acids build
A
triglycerides and other lipids like steroids
24
Q
functions of amino acids
A
protein function, neurotransmission, nitrogen metabolism, energy conversion, cell signaling
25
functions of nucleotides
energy conversion and metabolism, nucleic acid function, signal transduction, enzyme catalysis
26
functions of simple sugars
source of chemical energy, energy conversion, cell wall structure, cell recognition, nucleotide structure
27
functions of fatty acids
energy source and conversion, cell membranes, cell signaling
28
what does the structure of a macromolecule determine
its function ; the ways they interact with each other determines cellular activities and behaviors
29
what type of bond bonds atoms of macromolecules
covalent bonds
30
strong bonds formed by adjacent atoms sharing electrons ; strongest and hardest to break due to stability
covalent bonds
31
driving force for chemical bonding between atoms
octet rule / most stable form
32
what is the chemistry of life organized around
carbon
33
why is the chemistry of life organized around carbon
it is highly versatile in its' bonding ; it can form molecules of widely different sizes, shapes, and composition
34
carbon single bonds
H, O, N, C ; free rotation around bond unless carbon is attached to large or charged attachments
35
carbon double bonds
O, N, C ; shorter, more rigid
36
carbon triple bonds
N, C ; shorter, more rigid
37
what determines the polarity of a covalent bond
differences in electronegativity
38
electronegativity increasing trend
left to right, bottom to top
39
most electronegative atom
oxygen
40
the tendency of an atom to attract a bonding pair of electrons
electronegativity
41
common polar bonds
unequal share of electrons; O-H N-H
42
common nonpolar bonds
2 atoms of the same element or 2 different atoms that share electrons equally ; C-H C-C
43
what kind of charges do polar covalent bonds have
partial charges
44
electrostatic attractions between the oxygen of one water molecule and the hydrogen of another ; lifetime of each individual bond is short, when one breaks, another forms. in liquid water, bonds are constantly breaking and forming
hydrogen bonds
45
how many hydrogen bonds can a single water molecule form
4
46
average number of hydrogen bonds in liquid water molecules
3.4 due to continuous motion ; compared to ice which is fixed at 4 in a lattice structure
47
H-bond acceptor
electronegative atom --> N or O
48
H-bond donor
hydrogen is covalently bonded to another electronegative atom
49
do hydrogens bonded to carbons participate in hydrogen bonding
no ; weakly polar --> not enough charge distribution
50
where are hydrogen bonds found
alcohols, ketones, polypeptide backbones, DNA base-pairing
51
what does DNA base pairing make
double-stranded helix
52
when are hydrogen bonds the strongest
at a direct angle, which is oriented to maximize electrostatic interaction --> H atom and 2 sharing atoms are in a straight line, which puts the partial positive directly between the 2 partial negative charges. 180
53
where do electrostatic interactions occur
between functional groups
54
some atoms gain or lose electrons to give the atom a filled shell (become more energetically stable)
ion formation
55
bonds between oppositely charged atoms
ionic bonds
56
Na+
sodium ion ; Na has one electron in its' outer shell so it is easier for it to donate it rather than find 7 more to fill it
57
Cl-
chloride ion ; Cl has 7 electrons in its' outer shell so it is easier to gain one instead of lose 7 to complete shell
58
a dimensionless value that reflects the solvent in which the ionic interaction is taking place
dielectric constant
59
increased polarity = _______ dipoles = ________ dielectric constant = ________ force / strength of interaction
increased ; increased ; decreased
60
what environments are dielectric constants stronger in
less polar environments; but biology always occurs in water so the ionic bonds are weak and the covalent bonds are strong
61
______ distance = _______ denominator = weaker force --> ionic bonds only operate over short distances
increased ; bigger
62
does water readily dissolve charged biomolecules
yes --> due to charged functional groups
63
what does water form around the functional group charges
hydration layer
64
how do hydrophilic molecules dissolve
water replaces the interactions between solutes that link ions to each other with solute-water interaction ?
65
how does water dissolve salt
hydrating and stabilizing the ions and weakening the electrostatic interaction between them ; water counteracts ions' tendency to associate with each other
66
explain what happens when you drop salt into water
individual ions separate and become hydrated by a shell of water to form electrostatic interactions between partial charges of water and full charges of ions. dissolution occurs
67
when does hydrophobic exclusion occur
when nonpolar groups associate in an aqueous environment
68
force that water has on hydrophobic molecules that cause them to dissociate from each other ; molecules are NOT directly attracted to each other
starts with individual nonpolar molecules surrounded by water
turns into a complex of nonpolar molecules and has a reduced surface area
hydrophobic exclusion
69
why are nonpolar bonds hydrophobic
they are unable to form energetically-favorable hydrogen bonds in water, therefore there is no compensation for the breaking of water hydrogen bonds. water molecules will form an ordered structure around the hydrophobic molecule to maximize the number of h bonds that can take place between water molecules
70
what does hydrophobic exclusion restrict
the movement of many water molecules; therefore creates unfavorable entropy/disorder
71
what is the purpose of decreasing the surface area during hydrophobic exclusion
hydrophobic molecules pack together to decrease the surface area that must interact with water, which means there are fewer water molecules that must interface with nonpolar material that it can't interact with
72
why are hydrogen bonds formed between water molecules considered energetically favorable interactions
they stabilize the water molecule
73
how do polar bonds compensate for the lost h bonds when a molecule is dropped in water
with new interactions between water and the solute ; replace the original h bonds and makes it energetically favorable overall
74
an orchestra of short-range attractive forces between uncharged atoms ; weak transient attractions
van der Waal forces
75
what makes van der waal forces occur
temporary dipoles
76
a random variation in electron position around one nucleus that can create a transient dipole ; surrounding electron clouds influence each other
temporary dipole
77
point where attraction between 2 neighboring atoms is maximal ; lowest energy state
van der wall contact
78
highly ordered steady state where environment is different than surroundings. requires a constant investment of energy to maintain
homeostasis
79
potential energy in biological systems
chemical bonds and electrochemical gradients
80
the amount of potential energy in a chemical bond reflects the _______ of shared electrons between 2 bonded atoms
position
81
bonds with highest potential energy
longest, weakest bonds, equal electron sharing (nonpolar)
C-H
82
bonds with lowest potential energy
shortest, strongest bonds, unequal electron sharing (polar)
O-H
83
why do ____ bonds have the lowest potential energy?
polar; they are stabilized by one of the 2 atoms, resulting in lower potential energy
84
example of potential energy in an electrochemical gradient
Na+ gradient
85
why are electrochemical gradients a good source of potential energy?
concentration on one side of the membrane creates potential energy with position because the force of diffusion is driving the ions back toward equilibrium
86
kinetic energy in biological systems
radiant (sun) energy, molecular movement, thermal energy
87
constant random launching of atoms or molecules
thermal energy
88
average thermal energy of a group of molecules
temperature
89
what occurs when temperature is transferred between 2 objects
heat
90
increased temperature = ______ atomic motion = ______ kinetic energy
more ; more
91
energy transformations that follow the laws of thermodynamics
cellular reactions
92
1st law of thermodynamics
conservation of energy --> energy can be used by a system but is never used up, it is converted by a system into a new form
93
2nd law of thermodynamics
more disorder is the tendency of nature --> increased entropy is favorable, a process must somehow increase entropy of the universe in order to occur
94
why is waste removal a type of kinetic energy
unusable energy dissipates into its' surrounding environment which increases molecular movement --> increased disorder of surroundings when released
95
processes that ______ entropy in a cell can take place only when some of that energy is converted to ________ and released to ______ entropy of ________ to follow the 2nd law of thermodynamics
decrease ; heat ; increase
96
one that, once started, releases energy and continues without the input of energy
spontaneous process
97
what do spontaneous reactions release
free energy (G) (usable energy)
98
G ; the quantity of the energy transformations that occur as a reaction proceeds Gibbs free energy
Gibbs free energy
99
G(products) - G(reactants)
an expression for the magnitude of the driving force that causes a system to reach equilibrium
delta G
100
delta G of a spontaneous reaction, free energy is _______
negative, free energy is released
exergonic
101
delta G of a non-spontaneous reaction, free energy is ________
positive, input of free energy is required
endergonic
102
spontaneous reactions start with ______ energy reactants and end with ______ energy products
higher ; lower
103
non-spontaneous reactions start with ________ energy reactants and end with ________ energy products
lower ; higher
104
H ; kinds and numbers of chemcial bonds and non-covenant interactions broken and formed as a reaction proceeds forwards
enthalpy
105
S ; randomness / disorder
entropy
106
when a reaction happens at a constant ______, delta G is determined by the _____ change and then _____ change
temperature ; enthalpy ; entropy
107
spontaneous processes tend toward ______ disorder
more
108
when is entropy favorable?
increased entropy = favorable
109
entropy is increased when products are _____ disordered than reactants
more
110
does a spontaneous reaction favor a positive or negative delta S?
positive
111
if delta S is positive, ________ increases, thermodynamically _______
entropy ; favorable
112
what causes an increase in entropy?
increase in the number of molecules or conversation from solid to liquid or gas
113
why is more disorder favorable?
more molecules are produced, and molecules have more molecular movement/freedom of motion due to their physical state
114
a liquid has a _______ entropy than a solid
more favorable
115
what do changes in enthalpy reflect
differences in the potential energy of the molecules involved in a reaction
116
spontaneous processes tend toward the formation of more _____ bonds and interactions
stable
117
______ enthalpy is more thermodynamically favorable
decreased
118
_____ potential energy is more favorable
lower
119
what is an alternative to low potential energy for more stability?
many H-bonds
120
does a spontaneous reaction favor a positive or negative delta H?
negative
121
why is a _______ enthalpy change favorable?
negative ; decreasing enthalpy means a decreased bond energy, which produces products in a lower energy state
122
if delta H is negative, ________ decreases, thermodynamically _______
enthalpy, favorable
123
what do changes in enthalpy reflect?
differences in the potential energy of the molecules involved
124
example of a reaction where both entropy and enthalpy change is thermodynamically favorable
glucose oxidation ; increases entropy and decreases enthalpy
more polar covalent bonds are present
125
what does the magnitude of delta G depend on?
depends on the chemical reaction and how far from equilibrium the system is initially
126
delta G < 0
favorable in what direction?
forward
127
delta G < 0
endergonic or exergonic?
exergonic
128
delta G > 0
favorable in what direction?
reverse
129
delta G > 0
endergonic or exergonic?
endergonic
130
delta G = 0
favorable in what direction?
process occurs equally in both directions
131
what is the value of delta G when a system is at equilibrium?
0
132
what does delta G = 0 mean?
the system is at equilibrium and there is no net change in the concentration of the reactants and products
133
experimentally determined at biochemical standard conditions
ΔG°'
134
biochemical standard conditions
1 atm, 298 K, [products] and [reactants] = 1M, pH=7, [H2O] - 55.5 M
135
why is ΔG°' not always accurate?
sometimes a cell is not under standard conditions, and the concentrations of reactants and products are not always equal to each other
136
ratio of concentrations at equilibrium (delta G= 0)
Keq
137
what does a large Keq value mean?
what are the values of the numerator and denominator at equilibrium?
the reaction tends to proceed until reactants are almost entirely converted into products
numerator = large
denominator = small
138
what does a small ratio of Keq indicate?
delta G is bigger (there is a large driving force) because the reaction is far from equilibrium
139
the actual delta G of a reaction is a function of delta G know prime and the ______ of reactants and products in the cell
concentrations
140
DG when ratio prods/reactants > 1
DG = POSITIVE
141
DG when ratio prods/reactants < 1
DG = NEGATIVE
142
when can a positive DG knot prime STILL PROCEED in a cell?
when the ratio is less than 1 ; DG is negative
