Unit 1 (Ch. 1-7) Flashcards
1
Q
three concepts of biological science:
A
- life is made up of cells (cell theory)
- life evolves
- life processes information
2
Q
what was the first evidence of cells?
A
came from the invention of microscopes (1600s)
3
Q
two tenets to cell theory:
A
- all organisms are made up of cells
- all cells come from preexisting cells
4
Q
what did louis pasteur do?
A
observed that cells come from preexisting cells, not from spontaneous generation, which supports one tenet of the cell theory.
5
Q
why is the theory of evolution (life evolves) important to cell theory?
A
it explains where organisms come from and how they’re related, which therefore provides an explanation of where cells come from.
6
Q
why was it important that pasteur used one flask with an open mouth and one flask with a sealed mouth in his experiment?
A
the sealed flask was a swan-neck flask, so nutrient broth settled in the neck. this prevented air flow and therefore growth in the flask.
7
Q
what common characteristics do all cells share?
A
- use the same biochemical molecules
- plasma membrane made of phospholipids
- acquire and use ATP
- use nucleic acids for genetic material
8
Q
examples of organisms’ ability to process information:
A
- the central dogma
- conversion of energy/ATP in response to changing information about their environment
8
Q
cells are highly adapted to ________
A
fit specific niches. their environment and structure dictates their function
9
Q
cells acquire and use energy in ________
A
response to changing information about their internal/external state (environment)
10
Q
the most abundant elements found in organisms are:
A
Carbon, Hydrogen, Oxygen, and Nitrogen (CHON)
11
Q
why are some elements so biochemically abundant?
A
all of these elements (CHON + a few others) have unpaired electrons ini their valence shells so they will readily bond with other elements to fill their valence shells. this makes them very reactive
12
Q
carbon has a valence of ____ and likes to form ________
A
4; double bonds
13
Q
hydrogen has a valence of ____
A
1
14
Q
oxygen has a valence of ____
A
2
15
Q
nitrogen has a valence of ____ and likes to form ________
A
3; triple bonds
16
Q
biochemically important atoms readily form covelent bonds to _________
A
fill their valence shells and therefore achieve their most stable state
17
Q
electronegativity:
A
the tendency of an atom to attract electrons
18
Q
why is electronegativity important?
A
it dictates the type of bond formation based on the difference in electronegativity of 2 atoms
19
Q
small EN difference
A
nonpolar covalent bond
20
Q
medium EN difference
A
polar covalent bond
ex. ammonia, water
21
Q
large EN difference
A
ionic bond
22
Q
nonpolar covalent bond:
A
equal sharing of electron pairs between atoms
23
Q
polar covalent bond:
A
unequal sharing of electron pairs between atoms due to electronegativity differences; partial charges exists but the total charge = 0
24
ionic bond:
unequal electron sharing; one atom "steals" electron pair(s) from another atoms. atoms have full charge
ex. NaCl
25
cation:
loss of electron(s), positive charge
26
anion:
gain of electron(s), negative charge
27
electronegativity scale for biological atoms:
O >> N > C ≈ H
28
covalent bond:
2 atoms share one or more pairs of electrons
29
bond type correlates to amount of ________ and ability for _________
potential energy; bonds to be broken
30
nonpolar covalent bond characteristics:
high potential energy, bond length is longer and strength is weaker ---> easier to break apart (lower bond dissociation energy), high amount of energy released which can be used by cells.
31
why do most biological macromolecules have lots of nonpolar covalent bonds?
it allows for more energy/ATP to be acquired and used without lots of energy input to break the bonds
32
polar covalent bond characteristics:
low potential energy, bond length is shorter and strength is stronger ---> harder to break apart (greater bond dissociation energy), low amount of energy released
33
gibb's free energy
change in free energy associated with a chemical reaction
34
gibb's free energy equation
∆G = ∆H - T∆S
35
if ∆G < 0 :
reaction is spontaneous and exergonic; can proceed without addition
36
if ∆G > 0 :
reaction is non-spontaneous and endergonic; needs addition of energy to occur
37
the spontaneity of a reaction is determined by _________ and _________
enthalpy; entropy
38
∆H
change in enthalpy; change in potential energy of the system
39
∆H is high
non polar bonds, high PE
40
∆H is low
polar bonds, low PE
41
∆S
change in entropy, change in disorder of the system
42
carbon is a ________ in all ________ molecules
crucial atom; biochemical
43
all biochemical molecules contain:
carbon-carbon bonds or a carbon backbone
44
what does the chemical evolution hypothesis propose?
complex organic molecules arose from simple organic molecules
45
issue with CO2 abundance
carbon in CO2 is not very reactive because of polar covalent bonds and needs to undergo a redox reaction to reduce carbon, making carbon more reactive
46
reduction
gain of electrons
47
oxidation
loss of electrons
48
what do redox reactions explain?
the possible interactions of carbon on early earth
49
what was the first step in chemical evolution?
reducing carbon. this allows for more complex organic molecules to form
50
what does reducing carbon do?
make it more reactive
51
two models for how chemical evolution occurred:
prebiotic soup model and surface metabolism model
52
what provided energy for carbon redox reactions to occur?
sunlight; it can break apart H2 and CO2 bonds and generate free radicals
53
pH:
measure of concentration of H+ ions in a solution
54
water has a pH of ____
7, neutral pH; concentration of H+ is 10^-7 M
55
acids
donate H+ ions during a chemical reaction, lower pH (pH < 7)
56
bases
take up H+ ions during a chemical reaction, higher pH (pH > 7)
57
H+ concentration increases/decreases by _________ every pH step
10-fold, pH scale is logarithmic
58
the concentration of H+ ions in solutions determine...
wether acid-base reactions will occur
59
buffers
act to reduce pH changes of a solution, helps stabilize pH by taking up or donating H+ ions
60
example of a weak buffer
carbonic acid is a weak acid that gives up protons
61
why are buffers useful to organisms?
organisms don't like large pH changes and are dependent on proper pH for biochemical processes to occur correctly
62
amino acid structure
amino group, carboxyl group
63
ionized amino acid form
positive charge on nitrogen in amino group and negative charge on oxygen in carboxyl group; charges balance each other out
64
where does the ionized form of an amino acid occur?
in solutions with a neutral pH
65
R group ________ determines an amino acid's _________
structure; function
66
types of amino acids (3 of them):
non-polar, polar, and charged
67
non-polar amino acids
least likely to form H-bonds in water because R groups are non-polar; no polar covalent bonds or ability to H-bond on outside of R group structure
68
polar amino acids
likely to from H-bonds with water and interact strongly with it; has molecules with partial charges or ability to form H-bonds in R group
69
charged amino acids
R group has full negative or positive charge
2 types: acidic and basic
acidic amino acids have a negative charge on the R group because of H+ donation to solution
basic amino acids have a positive charge on the R group because of H+ uptake from solution
70
there is evidence for amino acid formation on early earth from ________
experimental simulations
71
ways amino acids may have formed on early earth (3 ways):
- underwater vents
- meteorite impacts/outer space
- chemical evolution in atmosphere and early oceans
72
isomer
same chemical formula, different chemical structure
73
optical isomers
2 molecules that are mirror images of each other/chiral
74
it is _________ _________ to get either optical isomer form of amino acids
equally likely
75
why doesn't glycine have an optical isomer?
it has a proton
76
most organisms only use ________ isomers to make proteins
left-handed
77
proteins are _______ of amino acids
polymers
78
proteins are formed by:
condensation reactions; produces H2O as a byproduct "monomer in, water out"
79
hydrolysis reaction
water used to break apart polymers "water in, monomer out"
80
peptide bonds
covalent bonds that link amino acids together, can have double bond properties because of electron sharing; links C of carboxyl group and N of amino group
81
a peptide strand has ________
polarity; N and C terminus
82
N-terminus
amino group end, nitrogen has positive charge
83
C-terminus
carboxyl group end, oxygen has negative charge
84
proteins have diversity in shape, structure, and function because...
peptide bonds can rotate
85
what does a polypeptide's amino acid sequence determine?
its' protein folding pathway
86
the stages of protein folding are ________ on each other
contingent
87
primary protein structure
linear sequence of amino acids
88
secondary protein structure
hydrogen bonding between carboxyl oxygen and amino hydrogen; forms α-helixes and β-pleated sheets
89
tertiary protein structure
interactions between R groups or R groups and peptide backbone
4 types of bonds:
- hydrogen bonding
- van der Waals/hydrophobic interactions
- disulfide bonding -> covalent bond between 2 different cysteines
- ionic bonding
90
quaternary protein structure
interactions between 2 different polypeptides
91
protein structure determines...
its function; proteins must fold correctly to function correctly
92
"oil drop" model
proteins can fold without help, will fold to minimize hydrophobic interactions
93
ways proteins get help with folding:
chaperones --> "grab" a protein and folds it
chaperonins --> create space for proteins to fold
94
prions
misfolded proteins that can cause disease; example of proteinopathy
95
nucleic acids are a polymer of ______
nucleotides
96
what is the structure of a nucleotide?
- pentose sugar (deoxyribose in DNA and ribose in RNA)
- nitrogenous base (A,T,C,G) , binds to 1' carbon
- phosphate group, binds to 5' carbon
97
nucleic acids are formed by ________ _______. these are called ________ _________.
condensation reactions; phosphodiester linkages
98
how is energy to link nitrogenous bases aquired?
originally a nucleotide has multiple phosphate groups, but all but 1 break off to generate energy for the reaction to occur
99
purines
A and G, 2 hydrocarbon rings, larger than pyrimidines
100
pyrimidines
C and T, 1 hydrocarbon ring
101
why do only purines bind to pyrimidines?
only this paring of nucleotides fits inside the double helix
102
pyrimidine problem
more purines found naturally and experimentally than pyrimidines
103
ribose problem
4 and 6 carbon sugars more likely to be made, but all nucleotides use ribose
104
Erwin Chargaff
discovered that A only binds to T and G only binds to C because of nucleic acid ratios, known as Chargaff's rule
105
Rosalind Franklin
discovered that DNA has a double helix structure through X-ray crystallography
106
Francis and Crick
discovered that DNA is antiparallel, this allows for optimal hydrogen bonding
107
DNA strands run ___ to ___
5' ; 3'
108
DNA's complimentarity allows for...
it to serve as a template for self-synthesis
109
where do site-specific proteins bind on DNA? why?
the major groove bc there is the most access to base pairs
110
where do non-specific binding proteins bind on DNA? why?
the minor groove bc there is the most access to the backbone
111
what are the differences between RNA and DNA?
- RNA has ribose as its sugar, the hydroxyl group instead of the -H allows for RNA to be flexible and have a high reactivity
- uracil instead of thymine
112
why is the flexibility of RNA important?
it can make a variety or secondary and tertiary shapes as its' complimentary to itself, which allows it to have several different functions
113
RNA world hypothesis
there may have been an intermediate phase between chemical evolution and the first life on earth where RNA catalyzed the formation of macromolecules
114
what does RNA primarily do today?
catalyzes peptide bond formation in ribosomes, it's required to make proteins
115
how are carbohydrates characterized?
by the presence of a carbonyl group
116
3 ways carbohydrates can vary:
- location of carbonyl group
- number of carbons
- arrangement of hydroxyl groups
117
aldose
carbonyl group on outside of carbohydrate
118
ketose
carbonyl group in middle of carbohydrate
119
aldose and ketose are _________
isomers
120
the arrangement of hydroxyl groups on a carbon chain can create ________
isomers
121
carbohydrates with 5 or more carbons can form...
a ring
122
alpha-glucose vs. beta-glucose
50/50 chance of forming either one during ring formation and contact of carbonyl and hydroxyl group
123
alpha-glucose
hydroxyl group oriented below plane of molecule
124
beta-glucose
hydroxyl group oriented above plane of molecule
125
glycosidic linkages form...
polysaccharides
126
what are glycosidic linkages
form from condensation reactions between hydroxyl groups
127
alpha-glycosidic linkage
forms between 2 alpha-glucose, linkage oriented downwards
128
beta-glycosidic linkage
forms between 2 beta-glucose, one monomer has to flip, linkage oriented upwards
129
alpha-glycosidic linkages are found in...
storage polysaccharides, they are easy for cells to break apart
130
examples of storage polysaccharides
starch, glycogen
131
starch
used in plant cells as storage
132
glycogen
used in animal cells as fat storage
133
beta-glycosidic linkages are found in... why?
structural polysaccharides; this is because the flipping of 1 monomer makes the polysaccharide sturdier and not as readily broken down by cells
134
examples of structural polysaccharides:
- cellulose
- chitin
- peptidoglycan
135
cellulose
primary component of plant cell walls, flipping of monomers allows for hydrogen bonds between chains
136
chitin
makes up exoskeleton of insects and crustaceans, component of fungi cell walls; flipping of monomers allows for hydrogen bonding between chains
137
peptidoglycan
primary component of bacterial cell walls, peptide bonds link chains which are stronger than hydrogen bonds
138
carbohydrates are formed from the __________ of carbon during ________
reduction; photosynthesis
139
photosynthesis
an endergonic process, requires energy to occur which is provided by sunlight
140
_________ of carbohydrates oxidizes carbon in ________ __________
hydrolysis; cellular respiration
141
cellular respiration
exergonic process, output of energy which makes ATP for use in endergonic reactions or by cells
142
carbohydrates have more ________ than CO2 because of an abundance of C-C and C-H bonds
potential energy
143
carbohydrates are a source of what?
stored chemical energy
144
the hydrolysis of carbohydrates can be used for...
formation of other macromolecules
145
carbohydrates are involved in...
cell-cell recognition, this is called glycocalyx
146
