Kaplan Biochem Flashcards
1
Q
in alpha amino acids, both the … and … groups are bound to the alpha carbon
A
amino; carboxyl
2
Q
not all amino acids have to have the amino and carboxyl groups .. –> GABA has the amino group on the gamma C
A
on the same C
3
Q
… amino acids: the 20 alpha amino acids encoded by DNA
A
proteinogenic
4
Q
only nonchiral/non-optically active amino acid: …
A
glycine
5
Q
all chiral amino acids used in eukaryotes are … amino acids
all except cysteine have … configuration
cysteine is ..
A
L
S
R
6
Q
nonpolar, nonaromatic aas: ... ... ... ... ... ... ... --> cyclic, conformationally strained
A
glycine alanine valine leucine isoleucine methionine proline
7
Q
aromatic aas:
…
…
… —> polar
A
phenylalanine
tryptophan
tyrosine
8
Q
polar aas: ... ... ... ... ... - has thiol that can participate in ... bonds
A
serine glutamine asparagine threonine cysteine; disulfide
9
Q
in cysteine, sulfur is larger and less electronegative than O –> leaves Cys susceptible to …
A
oxidation
10
Q
amide groups for Gln and Asn do not … – amides are relatively …
A
become charged; neutral
11
Q
acidic aas:
…
…
the negative charges on the anion forms of these aas form at … (…) –> these are the only 2 amino acids that have … on the side chains at physiological pH
A
aspartic acid
glutamic acid
physiological pH; 7.4; negative charges
12
Q
basic aas:
…
…
…
A
lysine
histidine
arginine
13
Q
pKa of histidine imidazole group is close to ….; at physiological pH, one N from the imidazole is … and the other is not
A
physiological pH; protonated
14
Q
all aas with … are hydrophilic –> more likely to be found on protein surface
… and … are also hydrophilic
A
charged side chains (acidic and basic aas)
asparagine; glutamine
15
Q
all nonpolar aas are … the rest have both … and …
A
hydrophobic; hydrophobic and hydrophilic character
16
Q
(three and one letter abbreviations)
alanine
A
ala, A
17
Q
(three and one letter abbreviations) arginine
A
Arg, R
18
Q
(three and one letter abbreviations) asparagine
A
Asn, N
19
Q
(three and one letter abbreviations) aspartic acid
A
Asp, D
20
Q
(three and one letter abbreviations) Cysteine
A
Cys, C
21
Q
(three and one letter abbreviations) glutamic acid
A
Glu, E
22
Q
(three and one letter abbreviations) glutamine
A
Gln, Q
23
Q
(three and one letter abbreviations) glycine
A
Gly, G
24
Q
(three and one letter abbreviations) Histidine
A
His, H
25
(three and one letter abbreviations) Isoleucine
Ile, I
26
(three and one letter abbreviations) leucine
Leu, L
27
(three and one letter abbreviations) Lysine
Lys, K
28
(three and one letter abbreviations) Methionine
Met, M
29
(three and one letter abbreviations) Phenylalanine
Phe, F
30
(three and one letter abbreviations) Proline
Pro, P
31
(three and one letter abbreviations) Serine
Ser, S
32
(three and one letter abbreviations) Threonine
Thr, T
33
(three and one letter abbreviations) Tryptophan
Trp, W
34
(three and one letter abbreviations) Tryosine
Tyr, Y
35
(three and one letter abbreviations) Valine
Val, V
36
amino acids are ...: they have both basic (amino) and acidic (carboxylic) groups that makes them able to either accept/donate a proton
amphoteric
37
in general: at low pH, ionizable groups tend to be ...
| at high pH, ionizable groups tend to be ...
protonated; deprotonated
38
pKa is the point at which the concentration of the protonated and deprotonated species are ... --> ...
equal; [HA] = [A-]
39
pH most groups will be ...
| pH > pKa --> most groups will be ...
protonated
| deprotonated
40
all aas have at least ... pKas bc they have 2 groups that can be protonated/deprotonated (amino and carboxyl)
pKa for carboxyl group is around ...
pKa for amino group is around ...
2
2
9-10
41
at physiological pH, the carboxyl group will be ... and the amino group will be ...
deprotonated; protonated
42
...: has both positive and negative charge but is electrically neutral as a whole --> ... ions
exist in water as ...
zwitterion; dipolar; internal salts
43
...: pH at which the molecule is electrically neutral
average of the ... values
aas with acidic side chains have relatively ... isoelectric points and those with basic side chains have relatively ... isoelectric points
isoelectric point
two nearest pKa values
low; high
44
...: small peptides, up to 20 residues
oligopeptides
45
peptide bond formation occurs as a .../... reaction
has partial ... character due to ... which restricts its ability to rotate
by convention, peptides are drawn with ... to the left and ... to the right and are read from left to right
condensation; dehydration; double bond; resonance; N-terminus; C-terminus
46
hydrolysis of peptide bonds in living organisms is ...
| e.g. trypsin and chymotrypsin --> cleave at specific peptides
enzymatically catalyzed
47
the secondary, tertiary, and quarternary structures a protein adopts is that which is most ... in a given environment
energetically favorable
48
primary sequence of a protein can be determined by ... -- most easily done by ... from which the protein derives
sequencing; sequencing the DNA
49
...: peptide chain coils clockwise around central axis --> ...
alpha-helix; right-handed
50
alpha helix
stabilized by ... between carbonyl oxygen and amide H ... residues away
side chains point ... helix core
significant secondary structure of ...
intramolecular H bonds
n+4
away from
keratin
51
...: either antiparallel or parallel
beta pleated sheets
52
beta sheets stabilized by both ... and ... H-bonds
intramolecular; intermolecular
53
due to its cyclic nature, proline would introduce a ... in the peptide chains when in the middle of alpha helices or beta sheets
only in alpha helices for something that will ..
Tends to be found at the ... in a beta pleated sheet and at the start of an alpha helix
kink; cross cell membrane; turns
54
... proteins: have structures that resemble sheets or long strands
e.g. ...
tend to serve ... purposes
fibrous;
collagen
structural
55
... proteins: tend to be spherical (like a globe)
e.g. ...
can be hormones, enzymes, etc. --> have more ... than the other category of proteins
globular
myoglobin
diverse roles (other category is fibrous)
56
...: intermediate states of protein folding
molten globules
57
when a solute dissolves in a solvent, nearby solvent molecules form a
solvation layer
58
when hydrophobic substances dissolve in water, water cannot ... effectively and so water molecules must arrange themselves into a more ... structure to maximize H bonding --> results in an ...
this is the basis for the ... that largely influence protein folding
hydrogen bond; ordered; unfavorable decrease in entropy; hydrophobic effect
59
when hydrophilic substances dissolve in water, ...
entropy is increased
60
quarternary structure roles:
can be more stable, by ... of the protein complex
can reduce amount of ... needed to ... protein complex
can bring ... close together
can induce ... (as in hemoglobin) or ... effects
reducing the surface area; DNA; encode; catalytic sites; cooperativity; allosteric
61
... proteins: derive part of their function from prosthetic groups
conjugated
62
... are permanently attached cofactors that can be organic molecules (e.g. vitamins) or metal ions -- necessary for enzyme function
prosthetic groups
63
...: proteins with lipid prosthetic groups
...: proteins with carb prosthetic groups
...: proteins with nucleic acid prosthetic groups
lipoproteins
glycoproteins
nucleoproteins
64
denaturation of proteins is often irreversible
| can be caused by ..., ..., ...
heat; solutes; pH
65
... is the individual amino acid Cys. ... is when two of them form a disulfide bond
cysteine; cystine
66
peptide bond is thermodynamically ...., but hydrolysis doesn't occur spontaneously in the cell because the ... is too high, such that hydrolysis is ...
unstable; activation energy; kinetically unfavorable
67
... are needed to catalyze peptide bond hydrolysis
enzymes
68
N amino acids --> ... peptide bonds
n - 1
69
... angle: angle of rotation of single bond between N and alpha C
... angle: angle of ration of single bond between carboxyl C and alpha C
phi
| psi
70
Gabriel synthesis of amino acids:
| ... is alkylated using base, then ..., and then .... to yield amino acid
N-phthalimidomalonic ester;
hydrolyzed
decarboxylated
71
strecker synthesis of amino acids:
starting materials: ..., ..., .../...
aldehyde reacts with ... to yield an ... ... is added to the imine to yield ... which is hydrolyzed to form the alpha amino acid
ammonia; KCN; aldehyde; ketone
| ammonia; imine; KCN; alpha-amino nitrile
72
...: catalyze redox rxns --> transfer of electrons between molecules
...: electron donor
..: electron acceptor
... or ... tend to be of this class
enzymes that have oxidase in their names use ... as the final electron acceptor
```
oxidoreductases
reductant
oxidant
dehydrogenases; reductases
oxygen
```
73
dehydrogenases remove a ... --> removing ...
hydride; electrons
74
...: catalyze movement of functional groups between two molecules
...: catalyze transfer of a phosphate group
transferases;
| kinases
75
...: catalyze breaking of a compound into two molecules by addition of water
tend to be named only for their ...
...: cleaves a phosphate group from another molecule
hydrolases; substrate
| phosphatase
76
...: catalyze cleavage of a single molecule into two products; don't require water
synthesis of two molecules into a single molecule can also be catalyzed by a lyase --> ...
lyases; synthases
77
...: catalyze rearrangement of bonds within a molecule
isomerases
78
...: catalyze addition/synthesis rxns, often require ATP
ligases
79
enzymes don't alter the ... for a reaction and do not change the ... of a rxn. they only affect ...
free energy change; equilibrium; rxn rates
80
... theory suggests that enzyme's active site is already in the appropriate conformation for the substrate to bind --> no ... necessary to form enzyme substrate complex
lock and key; conformational change
81
... model: conformational change of the enzyme is necessary for substrate binding to occur
induced fit
82
.../...: nonprotein molecules that bind to the active site of an enzyme and participate in catalysis
cofactors; coenzymes
83
...: enzymes without their cofactors
| ...: enzymes containing their cofactors
apoenzymes
| holoenzymes
84
...: generally inorganic molecules/metal ions --> ...
| directly participate in enzymatic rxn
cofactors; minerals
85
...: small organic groups --> ... and derivatives of these
coenzymes; vitamins
86
water-soluble vitamins: ... and ...
| fat-soluble vitamins: ..., ...., ..., ...
B; C
| A; D; E; K
87
fat-soluble vitamins regulated by ... -- quantify ability of a molecule to dissolve in a polar/nonpolar environment
partition coefficients
88
coenzymes act as a ... molecule
carrier
89
cofactors and coenzymes tend to be ... and usually carry a charge by ..., ..., or ...
usually in ..., ... concs in the cells
small; ionization; protonation; deprotonation
| low; tightly regulated
90
...: all enzymes bound to substrate
saturation
91
reaction rate can no longer increase once ... is achieved --> enzyme working at ...
saturation; maximum velocity
92
can only increase vmax by increasing
enzyme concentratio
93
... describes relationship between rate of reaction, enzyme, substrate, and product concs
equation: ... or ...
michaelis-menten
| v= (v_max*[S])/(K_m+[S]) or v= (k_cat*[E]*[S])/(K_m+[S])
94
Km is the substrate concentration at which .... (velocity is ...)
half of the enzyme's active sites are full; half-maximal
95
Km is ... --> lower Km = ... affinity of enzyme for its substrate --> ... conc of substrate required for 50% enzyme saturation
Km cannot be altered by changing .../... ...
Michaelis constant; higher; lower; enzyme/substrate concentration
96
when [S] < Km --> rxn rate ... when substrate is added
increases a lot
97
when [S] > Km and approaches Vmax --> rxn rate ... and is ... by addition of substrate
slows; not really affected so much
98
Vmax = ...
[E]*kcat
99
kcat is ... --> measures number of substate molecules converted to product, per enzyme molecule per second
... --> catalytic efficiency of an enzyme
turnover number
| Kcat/Km
100
```
... = double reciprocal of michaelis-menten; allows for easier graphical analysis of enzyme kinetics
X-int = ...
Y-int = ...
```
lineweaver-burk
-1/Km
1/Vmax
101
.... michaelis-menten plot indicates cooperativity among substrate binding sites (like Hgb)
sigmoidal
102
enzymes have ... state and ... state
in ..., binding of substrate to one subunit promotes ... transition of the other subunits, thus increasing their ... for the substrate
low-affinity tense; high-affinity relaxed
| cooperativity; T--> R; affinity
103
enzymes showing cooperative kinetics tend to be ... enzymes in pathways
cooperative enzymes subject to ... and ..., competitively and allosterically
regulatory; activation; inhibition
104
...: indicates degree of cooperativity
Hill's coefficient
105
Hill's coefficient
> 1 --> ... --> affinity ... in other subunits when substrate binds to one subunit
< 1 --> ... --> affinity ... in other subunits when substrate binds to one subunit
= 1 ---> ...
positively cooperative; affinity
negatively cooperative; decreases
no cooperativity
106
enzyme activity = enzyme ... = enzyme ...
velocity; rate
107
enzyme catalyzed rxns occur at an ...
rates tend to double for every ... increase until optimal is reached
optimal for human body is ...
optimal temp
10 degree C
37 degrees C
108
optimal pH for enzymes that circulate and function in human blood is ... --> ...
physiological pH; 7.4
109
pH < 7.35 --> ...
acidemia
110
in vitro, altering ... can disrupt hydrogen and ionic bonds, changing the ... of the enzyme, or ... it
salinity; conformation; denaturing
111
...: enzyme regulation facilitated by products further down a pathway
...: more rare scenario in which intermediates that precede the enzyme regulate it
.../... --> once there is enough of a given product, we turn off the pathway that creates the product
feedback regulation
feed-forward regulation
feedback inhibition/negative feedback
112
...: competitive, noncompetitive, mixed, uncompetitive
reversible inhibition
113
... inhibition: occupancy of the active site by a competitor of the substrate
overcome by ...
... is not altered, bc if enough substrate is added, it will outcompete the inhibitor and be able to run at the same one
... --> substrate conc has to be higher to reach half max velocity
competitive; adding more substrate
Vmax
increases apparent Km
114
...: inhibitor binds to allosteric site, inducing change in enzyme conformation
cannot be overcome by adding more substrate
bind equally well to ... and ...
... decreases bc there is less enzyme available to react
... stays the same bc active forms of enzyme retain same affinity for the substrate
noncompetitive inhibition
enzyme; enzyme-substrate complex
Vmax
Km
115
... inhibition: can bind to either enzyme/enzyme-substrate complex --> has a different affinity for each
if it were to have the same affinity, it would be a ... inhibitor
bind at an ...
mixed;
noncompetitive
allosteric site
116
mixed inhibition:
alter value of Km
if preferentially binds to enzyme-substrate complex, Km would ... bc it would cause the enzyme to bind more ... to the substrate
if preferentially binds the enzyme without the substrate, Km would ...
decrease; tightly
| increase
117
mixed inhibition:
Vmax is ..., again bc there is less enzyme available to react
on lineweaver-burk, intersection occurs at ...
decreased; point that is not on either axis
118
```
... inhibition: bind only to enzyme-substrate complex
Km ...
bind to ... site
... Vmax
shows as ... on lineweaver-burk
```
```
uncompetitive
decreased
allosteric
decreases
parallel lines
```
119
...: active site made unavailable for prolonged period of time/ enzyme is permanently altered
irreversible inhibition
120
regulated enzymes
...: allosteric inhibitors/allosteric activators can bind to enzyme
...: can be activated/deactivated by .../...
...: covalent attachment of sugar molecules
allosteric enzymes
covalently modified enzymes; phosphorylation; dephosphorylation
glycosylation
121
regulated enzymes:
...: enzymes that are secreted in an inactive form; these must be activated
have .. domain and ... domain
... domain must be removed/altered to expose the active site
zymogens; catalytic; regulatory
| regulatory
122
active sites create ... for the rxns that the enzyme catalyzes in that it essentially closes around the substrates, preventing interference from compounds outside of the enzyme
microenvironments
123
regulation of enzymes by phosphorylation is favorable for the following reasons:
creates ... that can disrupt old interactions and form new ones. can modify active site to allow for better interactions with substrate
negative oxygen grants active site ... properties that allows enzyme to interact with substrate in a more stabilizing way
net negative charge
| hydrogen bonding
124
regulation of enzymes by phosphorylation is favorable for the following reasons:
the speed at which phosphorylation occurs is adjustable by the cell --> ... is adjustable
... is abundant in the cell -- regulation by phosphorylation occurs ..., not really .. since there isn't much ATP there
kinetics
| ATP; intracellularly; extracellularly
125
regulation of enzymes by phosphorylation is favorable for the following reasons:
...: activated kinases can be used to regulate many rxn pathways, which can allow for amplification
amplification effects
126
regulation of enzymes by phosphorylation is favorable for the following reasons:
releases large amount of ...
phosphorylation is reversible using ...
free energy
| phosphatases
127
catalytic efficiency is limited by the rate at which the enzyme and substrate actually ... to form the ...
come together; enzyme-substrate complex
128
non competitive inhibition ... the turnover number of the enzyme
reduces
129
structural proteins generally have ... secondary structure and a ... -- a repetitive organization of secondary structural elements together sometimes referred to as a motif
highly repetitive; supersecondary structure
130
structural proteins:
... gives it a fibrous nature
...: trihelical fiber (three left-handed helices that form an overall right-handed helix) --> makes up most of the ... of connective tissue and provides ... and ..
regularity
| collagen; extracellular matrix; strength; flexibility
131
structural proteins:
...: part of extracellular matrix of connective tissue; provides stretch and recoil
...: intermediate filament in epithelial cells; contribute to mechanical integrity and function as regulatory proteins
elastin
| keratin
132
structural proteins:
...: makes up microfilaments and thin filaments in myofibrils --> most abundant protein in eukaryotic cells
... and ... side allows motor proteins to travel ... along actin filament
actin
positive; negative
unidirectionally
133
structural proteins:
...: makes up microtubules which provide structure, chromosome separation in mitosis and meiosis, and intracellular transport with kinesin and dynein
has ...: negative end of a microtubule is located adjacent to the ..., positive end in ... of a cell
tubulin
| polarity; nucleus; periphery
134
... proteins: display enzymatic activity, acting as ATPases to power ... change necessary for motility
interact with .../...
motor; conformational
| actin; microtubules
135
(motor proteins) ...: motor protein that interacts with actin; thick filament in myofibril; involved in cellular transport
has head and neck; neck movement contributes to ...
myosin; sarcomere contraction
136
(motor proteins) .. and ...: motor proteins associated with microtubules; have 2 heads, one of which is always attached to tubulin
kinesins; dyneins
137
(motor proteins) ...: align chromosomes during metaphase and depolymerize microtubules during anaphase
bring vesicles toward ... end of microtubule
in neurons, kinesins bring neurotransmitters toward ... end --> towards ...
kinesins
positive
positive
synaptic terminal
138
(motor proteins) ...: involved in sliding movement of cilia and flagella
bring vesicles toward ... end of microtubules
in neurons, bring neurotransmitters towards ... end --> back toward ...
dyneins
negative
negative
soma
139
...: transport or sequester molecules by binding to them
| Hgb, calcium-binding proteins, DNA-binding proteins (transcription factors), etc
binding proteins
140
binding proteins contd
| when sequestration of a molecule is goal, binding protein has ... across a ...
high affinity; variety of concentrations
141
binding proteins contd:
transport proteins tend to have varying affinity depending on ... --> whether it needs to ../... its target to maintain a steady-state
environment
| bind; unbind
142
...: proteins on most cell surfaces that assist in binding the cell to the extracellular matrix/other cells
cell adhesion molecules
143
cell adhesion molecules contd:
all ... proteins
...: glycoproteins that mediate calcium-dependent cell adhesion --> different cells have ...
integral membrane proteins
cadherins
type-specific cadherins
144
cell adhesion molecules contd:
...: group of proteins that all have two membrane-spanning chains, alpha and beta, involved in binding to and communicating with the extracellular matrix
important for ...
can promote .., ..., etc
integrins
cellular signaling
cell division; apoptosis
145
cell adhesion molecules contd:
...: bind to carbs that project from other cell surfaces --> form the weakest bonds of the cell adhesion molecules (that is, this one compared to cadherins and integrins)
important in ....
selectins; host defense
146
immunoglobulins:
| ... and ... interactions hold heavy and light chains together
disulfide linkages; noncovalent interactions
147
...: cells receive and act on signals; take advantage of either existing gradients or second messenger cascades
proteins participate by acting as .., ... for facilitated diffusion, ..., and ...
```
biosignaling
extracellular ligands
transporters
receptors
second messengers
```
148
....: proteins that create specific pathways for charged molecules
allow for ...
ion channels
| facilitated diffusion
149
ion channels:
...: unregulated --> based solely on conc gradient
...: gate is regulated by the membrane potential change near the channel (e.g. nonspecific sodium-potassium channels work in sinoatrial node of heart to bring cell back to threshold when voltage drops)
..: requires the binding of a ligand to open/close the channel
ungated channels
voltage-gated channels
ligand-gated channels
150
ion channels contd:
kinetics of transport can be derived from ...--> Km here would refer to ... at which transporter is functioning at half of its maximum velocity
michaelis-menten
| solute conc
151
...: membrane receptors that have catalytic activity when ligands bind
enzyme-linked receptors
152
enzyme-linked receptors:
...: anchors receptor to cell membrane
...: stimulated by ligand to induce a conformational change that activates catalytic domain
membrane-spanning domain
| ligand-binding domain
153
enzyme-linked receptors:
binding of ligand initiates a ...
...: contains monomer and when ligand binds, they dimerize and this dimer can phosphorylate other enzymes
second messenger cascade
| receptor tyrosine kinases
154
...: integral membrane proteins involved in signal transduction
G-protein coupled receptors
155
G-protein coupled receptors:
have ... membrane spanning alpha helices
use a ... protein -- intracellularly linked to guanine nucleotides
ligand binding ... of receptor for G protein, activating the protein
Yeah 7
heterotrimeric G protein
increases affinity
156
G-protein coupled receptors:
Gs --> stimulates ..., ... [cAMP]
Gi --> inhibits ...., ... [cAMP]
adenylate cyclase; increasing
| adenylate cyclase; decreasing
157
G-protein coupled receptors:
| Gq --> activates ..., which cleaves ... from the membrane to form PIP2 which is cleaved into ... and ...
phospholipase C; phospholipid; DAG; IP3
158
G-protein coupled receptors:
| IP3 can open .. --> increases ... in the cell
calcium channels
| [Ca2+]
159
G-protein coupled receptors:
G proteins have ..., ..., and ... subunits
... subunit binds GDP in its inactive form and is complexed with the other two subunits
when a ligand binds, GDP is replaced with ... and the ... subunit dissociates --> this subunit .../... ...
alpha; beta; gamma
alpha
GTP; alpha
activates/inhibits adenylate cyclase
160
...: crushing, grinding, or blending tissue of interest into an evenly mixed solution
homogenization
161
... can isolate proteins from smaller molecules before other isolation techniques are used
centrifugation
162
both .... and ... can be used for native/denatured proteins
electrophoresis; chromatography
163
electrophoresis subjects compounds to an electric field to move them according to ... and ...
net charge; size
164
...: directly proportional to electric field strength (E) and net charge on the molecule (z) and is inversely proportional to a frictional coefficient (f), that depends on mass and shape of migrating molecules
migration velocity
165
migration velocity: v =
Ez/f
166
...: porous gel that allows for separation based on size and charge
molecules will move fastest if they are ..., ... charged, or placed in a ...
molecules will move slower/not at all if they are ... and .., electrically ..., or in a ...
polyacrylamide gel;
small; highly; large electric field
bigger; convoluted; neutral; small electric field
167
...: used for analyzing proteins in native states
limited by the fact that there are varying ... and ... ratios of proteins that may cause multiple proteins to experience same level of migration
polyacrylamide gel electrophoresis
| mass-to-charge; mass-to-size
168
polyacrylamide gel electrophoresis
| most useful in comparing size/charge of proteins known to be ...
similar in size
169
polyacrylamide gel electrophoresis
SDS-PAGE:
sodium dodecyl sulfate is used to make charge for all proteins ..., such that ... is the differentiating factor
it disrupts ... interactions
uniform; molecular mass
| noncovalent interactions
170
polyacrylamide gel electrophoresis
...: separation of proteins based on isoelectric point
mix of proteins is placed in a gel with a ... (acidic at ..., and basic at ..., ... in the middle)
when proteins reach part of gel, where the pH = pI, the protein becomes ..., and thus stops moving
isoelectric focusing
pH gradient; anode; cathode; neutral
electrostatically neutral
171
... allows for isolated proteins to be immediately available for identification and quantification
chromatography
172
chromatography:
the more similar the compound is to its surroundings, the more it will ... and move ... through its surroundings
preferred over electrophoresis when ... are beings separated
stick to; slowly; large amounts of protein
173
chromatography:
sample is placed on ... (aka ...). a ... phase is run through, allowing the sample to run through (...) the stationary phase
solid stationary phase; adsorbent; elute
174
chromatography:
if sample has high affinity for stationary phase, it ...
if it has high affinity for mobile phase, it ...
won't move much
| will move quickly
175
chromatography:
... amount of time a compound spends in the stationary phase
...: separation of compounds within the stationary phase that results from varying retention times
retention time
| partitioning
176
chromatography:
| common properties used for separation: ..., ..., ...
charge
pore size
specific affinities
177
(column chromatography) column filled with ... as adsorbent
| ... and ... determine migration velocity
silica/alumina beads
| size; polarity
178
(column chromatography) less polar the compound the ... it elutes through the column
solvent drips out at the end of the column and different fractions that leave the column can be collected. these fractions contain ... that differentiate them
faster
| bands
179
(column chromatography) ... + ... is kept and the solvent is ...
can be used to separate and collect ... besides proteins (e.g. nucleic acids)
solvent; compound of interest
| macromolecules
180
(ion-exchange chromatography) beads in column coated with ...
after all other compounds have moved through the column, a ... is used to elute the charged molecules that have stuck to the column
charged substance;
| salt gradient
181
(size-exclusion chromatography) ... of various sizes are used
... get stuck in these and thus move more slowly
size of pores can be varied so that molecules of ... can be fractionated
common approach in protein purification is to use an ... followed by a ...
porous beads
small compounds
different molecular weights
ion-exchange column; size-exclusion column
182
(affinity chromatography)
coating beads with ... that binds protein/specific antibody to the protein, such that protein is ... in column
common stationary phase molecules include ... (used in separation of genetically engineered proteins with histidine tags), ..., ..., ...
```
receptor
retained
nickel
antibodies
antigens
enzyme substrate analogs
```
183
(affinity chromatography) once protein is retained, it can be eluted by washing column with ...
eluents can also have specific ... or ... that disrupts bonds between ligand and protein of interest
drawback: recovered substance can be ...
free receptor
pH; salinity level
bound to the eluent
184
protein structure can be determined through ... and ...
... more common and reliable --> measures e- density on a high resolution scale; can also be used for nucleic acid -- generates ... that can be used to determine structure
X-ray crystallography; nuclear magnetic resonance spectroscopy
diffraction pattern
185
... can be used to determine the primary sequence of small proteins:
for sequences of up to ...-... aas
selectively and sequentially removes ... of the protein, which is subsequently analyzed using ...
Edman degradation
50-70
N-terminal aa
mass spec
186
... (..., ..., ...) can also selectively cleave proteins, creating smaller fragments that can be analyzed via Edman or electrophoresis
positions of ... and .. cannot be determined by these methods since they reduce protein to primary structure
proteases; chymotrypsin; trypsin; cyanogen bromide
| disulfide links; salt bridges
187
...are determined by following the process of a known rxn, often accompanied by a ...
activity levels for enzymatic samples; color change
188
... can be used for proteins, since they have aromatic side chains
drawback: sensitive to contaminants
UV spec
189
proteins cause ... changes with certain rxns
... (BVA) assay
... reagent assay
... protein assay --> more reliable and simpler
colorimetric;
bicinchoninic acid
Lowry reagent
Bradford
190
bradford protein assay:
mixes protein with ... dye, which turns blue in presence of protein
higher protein conc = larger conc of ...
samples of known protein concs are reacted with the bradford reagent to create a ... that is then used to determine unknown protein concs
not very accurate when more than one proteins present
coomassie brilliant blue
blue dye
standard absorbance curve
191
...: basic structural units of carbs
| simplest monosaccharides are trioses - 3-C sugars
monosaccharides
192
...: carbs with an aldehyde as their most oxidized functional group
...: carbs that have ketones as their most oxidized functional group
aldoses
| ketoses
193
carbonyl C in carbs is always ... ( if aldehyde) or ... (if ketone), because it is the most oxidized
C-1; C-2
194
aldehyde C/ketone C can participate in ... --> sugars in these linkages are ...
glycosidic linkages; glycosyl residues
195
simplest ketose: ...
dihydroxyacetone
196
...: determined by the three dimensional arrangement of the groups attached to the chiral C
enantiomers have ... absolute configs
absolute configuration
| opposite
197
number of stereoisomers = ..., where n is the number of chiral Cs
2^n
198
not all carbs labeled as D have ... optical rotation and not all that have L are ... this is just for ...
optical activity is determined ...
+; -
glyceraldehyde
optical activity
199
Fischer projections:
horizontal lines are ..., vertical lines are ...
in this projection, D-C have their highest numbered OH group on the ... and L-carbs have their highest numbered OH group on the ...
wedges; dashes
| right; left
200
...: same sugars, in different optical families --> configuration at every chiral center is switched
enantiomers
201
...: two sugars that are in the same family, but are not identical and are not mirror images of each other --> only configurations at some chiral Cs are switched
diastereomers
202
...: diastereomers that differ only in the configuration of one chiral C
epimers
203
a compound can have only one ..., but can have multiple ..
enantiomer; diastereomers
204
carbs can undergo intramolecular rxns to form cyclic ... and ...
carbonyl C becomes chiral --> ... C
...: OH on C1 is trans relative to CH2OH group
...: OH on C1 is cis relative to CH2OH group
hemiacetals; hemiketals
anomeric
alpha-anomer
beta-anomer
205
... rings: six-membered rings
| ... rings: five-membered rings
pyranose
| furanose
206
...: useful for describing 3D conformation of cyclic structures
groups on the right in a Fischer projection will point ... on a Haworth projection
Haworth projection
| down
207
in water, hemiacetals will cycle between the ... and ... forms (bc of hydrolysis of the hemiacetal and then reformation of the ring) --> this allows it to spontaneously change its conformation as ... or ... --> ...
open; closed
alpha; beta;
mutarotaiton
208
mutarotation can be catalyzed by .../... and leads to mixture of alpha and beta anomers at ...
... anomer of glucose is more stable, so equilibrium is ...% alpha and ...% beta --> hydroxyl is ... in eta
```
acid; base
equilibrium concs
beta
36; 64
equatorial
```
209
in the open-chain forms, carbs can be ...
aldehyde oxidation yields ...
aldehydes are considered ... bc they can be oxidized
oxidized
aldonic acids
reducing agents
210
any monosaccharide with a hemiacetal ring is a ... sugar
| oxidation of aldose in ring form yields ... --> cyclic ester with carbonyl group on the anomeric C -- ... is a lactone
reducing
lactone
vitamin C
211
reagents that detect presence of reducing sugar --> ... and ...
...: silver nitrate is mixed with NaOH to produce ..., which is dissolved in ammonia to produce [Ag(NH3)2]+ --> produces .. when aldehydes are present, indicating that sugar is reducing sugar
...: aldehyde group is oxidized, yielding a red precipitate of ...
```
Tollen's; Benedict's
Tollen's
silver oxide
silvery mirror
Benedict's
Cu2O
```
212
... can be used to test for glucose, because it doesn't react with other reducing sugars
glucose oxidase
213
more reactive oxidizing agents (e.g. dilute nitric acid) will oxidize the aldehyde and the primary alcohol to ..
carboxylic acids
214
... are also reducing agents --> can be ... to form ... and subsequently oxidized
ketose sugars; tautomerized; aldoses
215
...: rearrangement of bonds in a compound, usually by moving a hydrogen and forming a double bond
...: compound with a double bond and an alcohol group
tautomerization
| enol
216
...: when aldehyde group is reduced to an alcohol
alditol
217
...: contains a hydrogen that replaces a hydroxyl group on that sugar (e.g. deoxyribose)
deoxy sugar
218
carbs can react with carboxylic acids and their derivates to form ...
estes
219
esterification is similar to ... of carbs, wherein a phosphate ester is formed
phosphorylation
220
hemiacetals react with alcohols to form ...
the subsequent C-O bonds are ... bonds and the acetals are ...
This rxn is essentially how we make larger saccharides
same happens with hemiketals to form ...
acetals
glycosidic bonds
glycosides
ketals
221
glycoside formation is a ... rxn, and breaking a glycosidic bond therefore requires ...
dehydration rxn
| hydrolysis
222
glycosides derived from furanose rings = ...
| glycosides derived from pyranose rings= ...
furanoses
| pyranosides
223
formation of an alpha or beta glycosidic linkage is nonspecific in that the anomeric C on one monosaccharide can react with ... --> glycosidic linkages are thus described by the ... of the Cs between which the bond is formed along with the ... of the anomeric C
if a glycosidic bond is formed between two anomeric Cs, the ... of both anomeric Cs must be in the name (e.g. alpha, alpha-1,1 linkage)
any of the alcohols on another monosaccharide
numbers
configuration
configuration
224
important disaccharides: ..., ..., ...
sucrose; lactose; maltose
225
sucrose: ....
lactose: ...
maltose: ...
glucose-alpha-1,2-fructose
galactose-beta-1,4-glucose
maltose: glucose-alpha-1,4-glucose
226
...: long chains of monosaccharides linked by glycosidic bonds
...: polymer of just one type of monosaccharide
...: made up of more than one type of monosaccharide
polysaccharides
homopolysaccharide
heteropolysaccharide
227
polysaccharides:
polymer formation can be .../... since glycosidic bonding can occur at multiple OH groups
...: when an internal monosaccharide in a polymer forms at least 2 glycosidic bonds
linear; branched
| branching
228
important polysaccharides:
| ...: main structural component of plants, present in their cell walls
cellulose
229
cellulose:
... --> beta-1,4 polymer of D-glucose
humans can't digest it because we don't have ...
acts as a source of ... for humans --> draws water into gut
homopolysaccharide
cellulase
fiber
230
...: linked alpha-D-glucose monomers
starches
231
plants store starch mostly as .. --> ... linkages
amylose; alpha-1,4
232
...: type of starch that is branched via alpha-1,6 linkages (Still has alpha-1,4 on the "main' chain)
amylopectin
233
starches:
... is used to test for presence of starch
enzymatically broken down to be used as ..
... cleaves amylose at nonreducing end to produce maltose
... cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, glucose
... help degrade amylopectin
```
iodine
energy source
beta-amylase
alpha-amylase
debranching enzymes
```
234
...: carb storage unit in animals; highly branched
glycogen
235
glycogen:
like starch, but has more ...
branching optimizes ..., makes it more ... as well and allows more ...
alpha-1,6 glycosidic bonds
energy efficiency; soluble
glucose storage
236
glycogen:
enzymes can work on many sites within the molecule at the same time since it's so ...
...: cleaves glucose from nonreducing end and phosphorylates it to form glucose-1-phosphate
highly branched
| glycogen phosphorylase
237
highly branched structure of amylopectin (same for glycogen) decreases ... between polysaccharide polymers and increases interaction with the ..., which makes it more soluble
intermolecular bonding; surrounding solution
238
membrane lipids are ... --> both hydrophobic and hydrophilic
amphipathic
239
...: have phosphate and alcohol that comprise polar head group, joined to hydrophobic fatty acid tail by phosphodiester linkages
phospholipids
240
phospholipids:
fatty acids are attached to a backbone to form ... region
classified according to the ....
glycerol forms .../...
sphingolipids have a ... backbone (not all sphingolipids are phospholipids)
hydrophobic tail
backbone
phosphoglycerides; glycerophospholipids
sphingosine
241
fatty acid tails of phospholipids vary in degree of ... and ... --> these behaviors determine behavior
saturation; length
242
...: no pi bonds, greater van der Waals forces, more stable structure --> solids
...: contains double bonds, which kink the fatty acid chain --> . liquids
... make up more fluid portions of the phospholipid bilayer
saturated fatty acids
unsaturated fatty acids
unsaturated phospholipids
243
glycerophospholipids contain .... backbone and are bonded to a polar head group and to two fatty acid tails
named according to their ... (e.g. phosphatidylcholine has a choline head group)
important to ..., ..., and ...
glycerol
head group
cell recognition; signaling; binding
244
the cell surface antigens on RBCs that dictate blood type are ...
sphingolipids
245
sphingolipids are involved in biological recognition at the
cell surface
246
sphingolipids have .../... backbone
| many sphingolipids are phospholipids bc they contain a ... linkage, but some contain ... linkages to ...
sphingosine/sphingoid
phosphodiester
glycosidic
sugars
247
...: any lipid linked to a sugar
glycolipid
248
...: simplest sphingolipid, has single H as head group
ceramide
249
..: major class of sphingolipids that are also phospholipids
have either phosphatidylcholine or phosphatidylethanolamine head group
head groups have ... net charge
major components in plasma membranes of cells producing ... --> ... and ... cells
sphingomyelins
no
myelin; oligodendrocytes; Schwann
250
...: sphingolipids with glycosidic linkages to sugars
NOT phospholipids
found on the outer surface of ...
glycosphingolipids
| plasma membrane
251
glycosphingolipids:
...: glycosphingolipids with a single sugar
...: glycosphingolipids with two or more sugars
...: no net charge at physiological pH
cerebrosides
globosides
neutral glycolipids
252
...: most complex sphingolipids
have polar head groups composed of oligosaccharides with one or more ... (... acid)
have a ... charge
gangliosides
N-acetylneuraminic acid; sialic
negative
253
gangliosides are ... as well
| important for ..., ..., and ...
glycolipids
| cell interaction, recognition, and signal transduction
254
...: esters of long-chain fatty acids with long-chain alcohols
function as protection:
for plants, prevent excessive ... and protect against ...
for animals, prevent ... and act as a ...
waxes
evaporation; parasites
dehydration; lubricant
255
lipids serve as coenzymes in the ... and in ... rxns
electron transport chain; glycosylation
256
lipids function as .... and ...
hormones; intracellular messengers
257
...: lipids built from isoprene moieties (C5H8), and have carbons grouped in multiples of ...
strongly scented
one terpene unit contains ...
terpenes
five
2 isoprenes
258
... = two isoprene units (1 terpene unit)
... = 3 isoprene units (1.5 terpene units)
... = 4 isoprene units (2 terpene units)
... = 6 isoprene units (3 terpene units)
carotenoids are ... (have 8 isoprenes, 4 terpenes)
```
monoterpenes
sesquiterpenes
diterpenes
triterpenes
tetraterpenes
```
259
triterpenes -- can be converted to ... and other ...
cholesterol; steroids
260
...: derivatives of terpenes that have been oxidized/rearranged
also strongly ..
named in the same way as terpenes, according to number of isoprene units
terpenoids
| scented
261
... and ... are precursors that feed into various biosynthetic pathways that produce important products
terpenes; terpenoids
262
...: metabolic derivatives of terpenes, have 4 cycloalkane rings fused together
steroids
263
steroids have ... and ...
| functionality is determined by ... status and ... present
3 cyclohexane; 1 cyclopentane
| oxidation; functional groups
264
...: steroids that act as hormones (e.g. testosterone)
steroid hormones
265
...: steroid that mediates membrane fluidity
...
at low temps, ... membrane fluidity
at high temps, ... membrane fluidity, preventing it from becoming too permeable
cholesterol
amphipathic
increases
decreases
266
cholesterol is precursor to some ..., ..., and ...
steroid hormones; bile acids; vitaminD
267
...: 20-C molecules that are unsaturated carboxylic acids derived from arachidonic acid
contain one ... C ring
prostaglandins
| 5C
268
prostaglandins:
.../... molecules
regulate the synthesis of ...
can have effects on ... function, ... cycle, and ... associated with fever and pain
paracrine/autocrine signaling
cAMP
smooth muscle; sleep-wake; elevation of body temps
269
...: essential nutrient that is not adequately synthesized by the body and thus, must be obtained in a dietary manner
vitamin
270
lipid-soluble vitamins are stored in ...
excess water-soluble vitamins are ...
fat soluble vitamins are: ..., ..., ..., and ...
fat
excreted
A; D; E; K
271
vitamin A (carotene): unsaturated hydrocarbon plays a role in .., ... and ..., and ... function
vision; growth; development; immune
272
vitamin A:
aldehyde form is ... -- component of light-sensing molecular system in the human eye
...: storage form of vitamin A, oxidized to retinoic acid -- hormone that regulates gene expression during epithelial development
retinal
| retinol
273
vitamin D (...): consumed/formed in ... driven rxn
cholecalciferol; UV
274
vitamin D:
converted to ... in liver and kidneys --> increases ... and ... uptake in intestines and thus promotes ... production
lack of vitamin D is cause of is cause of ... -- impeded growth, underdeveloped bones in children
calcitrol; Ca2+; phosphate
bone
rickets
275
vitamin E: characterizes group of closely related lipids called ... and ... --> have a substituted aromatic ring with long isoprenoid side chain and are hydrophobic
tocopherols; tocotrienols
276
vitamin E:
| ...: biological antioxidants --> destroy free radicals to prevent oxidative damage
tocopherols
277
...: a group of compounds including phylloquinone and menaquinone
vital to posttranslational modifications required to form ... - clotting factor in the blood
vitamin K
| prothrombin
278
aromatic ring of vitamin K undergoes cycle of ... and ... during the formation of prothrombin
vit K is required to introduce ... on some calcium dependent proteins
oxidation; reduction
| calcium binding sites
279
...: lipids specifically used for energy storage
triacylglycerols
280
lipids are better than carbs for energy storage:
fatty acids are more ... than sugars --> C in fatty acids have more ..., and oxidation allows electrons to move from ... to more ... atom, which is stabilizing and releases energy
reduced
electron density
less electronegative
electronegative
281
oxidation of triacylglycerols yields ... the energy per gram as carbs
twice
282
lipids:
triacylglycerols are ... --> don't require water for stability, which decreases their weight
dual benefit as ... and ...
hydrophobic
| energy storage; insulation
283
... (...): three fatty acids bonded by ester linkages to glycerol
rare for all three fatty acids to ...
... and ... --> polar hydroxyl groups of the glycerol component and polar carboxylates of fatty acids are bonded together, ...
triacylglycerols; triglycerides;
be the same
nonpolar; hydrophobic
decreasing their hydrophilicity
284
triacylglyerols:
deposits are seen in cells as ... in cytosol -- can be recruited when the cell needs additional energy to divide/survive
...: cells that store large amounts of fat, found primarily under the skin, around mammary glands, and int he abdominal cavity
oily droplets
| adipocytes
285
triacylglycerols:
in plants, are present in seeds as ..
travel bidirectionally between ... and ... in the bloodstream
physical characteristics primarily determined by ... of fatty acid chains
oils
liver; adipose tissue
degree of saturation
286
free fatty acids: unesterified fatty acids with a free ...
| circulate in the blood bonded noncovalently to ....
carboxylate group
| serum albumin
287
...; ester hydrolysis of triacylglycerols using a strong base (such as lye-sodium or potassium hydroxide)
cleaves the fatty acid, leaving the ... of the fatty acid and glycerol
fatty acid salt = ...
saponification
sodium salt
soap
288
soaps act as ... --> lowers surface tension at surface of a liquid, serving as detergent/...
surfactants
| emulsifier
289
soaps act as surfactants:
with solutions that are in two separate phases, addition of soap would "combine" them into one phase, forming a ... --> this is due to formation of ...
colloid; micelles
290
...: tiny aggregates of soap with the hydrophobic tails turned inward and the hydrophilic heads turned outward, which allows for overall solvation
micelles
291
nonpolar compounds can dissolve in the ... of the water-soluble micelle
hydrophobic interior
292
micelles are biologically important --> absorption of fat-soluble ... and complex ... like ...
... and ... secreted by gallbladder form micelles that increase SA available for lipolytic enzymes
vitamins
lipids; lecithins
fatty acids; bile salts
293
DNA is a ... made of ... --> polymer
polydeoxyribonucleotide; monodeoxyribonucleotides
294
nucleosides: a ... bonded to a ... and formed by covalently linking C-1' of the sugar to the base
C atoms in the ... are labeled with ' to distinguish from C atoms in ...
pentose sugar; nitrogenous base
| sugar; base
295
...: when one or more phosphate groups are attached to C-5' of a nucleoside
nucleotides
296
molecules like ATP are high-energy compounds bc of the energy associated with the ... between closely associated negative charges on the phosphate groups
repulsion
297
nucleic acids classified according to the ... they contain --> ribose = ..., deoxyribose (ribose with ... OH replaced with H) = ...
pentose
RNA
2' OH
DNA
298
backbone of DNA is composed of alternating .... and ... groups which determines its directionality --> always read from 5' to 3'
nucleotides are joined by ... bonds
sugar; phosphate; 3'-5' phosphodiester bonds
299
phosphate group links ... C of one sugar to the ... phosphate group of the next incoming sugar in the chain
phosphates carry ..., and thus so does DNA and RNA
3'; 5'
| negative charge
300
distinct 5' and 3' ends gives DNA backbone ...
| 5' end of DNA will have an .../... group bound to C'5' of the sugar, while 3' end has a ... on C-3' of the sugar
polarity
OH/phosphate
free OH
301
purines: have ... rings in their structure
two purines in nucleic acids are ...and ...
PURe As Gold
2
| adenine; guanine
302
pyrimidines: have only ... ring in their structure
..., ..., and ...
CUT the PYe
one
| cytosine; thymine; uracil
303
purines and pyrimidines are ... heterocycles
aromatic
304
aromaticity qualifications:
compound is ..., ..., and...
compound has ... pi electrons --> ... rule
stable due to delocalization of electrons, and thus, are pretty unreactive
cyclic; planar; conjugated
| 4n+2; Huckel's
305
Bc of ..., nucleic acids are very stable --> why they are ideal for storing genetic information
aromatic nature
306
Watson-Crick model: presented 3D structure of DNA and indicated that DNA is a ...
...: two linear polynucleotide chains of DNA are wound together in a spiral orientation along a common axis
two strands of DNA are ...
double helix
double helix
antiparallel
307
.... is on the outside of the helix with the ... on the inside
sugar-phosphate backbone; nitrogenous bases
308
...: A always with T and G always with C
| G and C have ... H bonds, which makes the G-C interaction stronger than A-T which only has ... H bonds
complementary base pairing
| 3; 2
309
The ... and the ... between bases provide stability to the double helix structure
H bonds; hydrophobic interactions
310
...: total purines will be equal to total pyrimidines overall, since %A = %T and %G = %C
Chargaff's rule
311
most DNA is a ... helix --> ....-DNA
makes a turn every 3.4 nm and has ... bases within that span
has ... and ... between the interlocking strands that are often the site of protein binding
right-handed helix; B
10
major and minor grooves
312
...-DNA --> zig-zag appearance, left-landed helix
| 4.6 nm and contains ... bases within that span
Z-DNA; 12
313
Z-DNA:
high ... conc or high ... conc can contribute to the formation of this form of DNA
No ... contributed to it yet bc its unstable and hard to research
G-C; salt
| biological activity
314
Double helix of DNA can be denatured by conditions that disrupt .... and ...
none of the ... links between nucleotides in the backbone of the DNA break during this process
achieved via ..., ..., and chemicals like ... and ...
H bonding; base-pairing
covalent
heat; alkaline pH; formaldehyde; urea
315
denatured single stranded DNA can be ... if denaturing condition is slowly removed
important for ... and detection of specific DNA sequences
reannealed
| PCR
316
...: DNA with known sequence
can be added to mix of target DNA sequences, and when it binds to target, may provide evidence of gene of interest --> ...
probe DNA; hybridization
317
DNA of chromosomes is wrapped around a group of small basic proteins called ... to form chromatin
histones
318
two copies each of the histone proteins ..., ..., ..., and ... form a histone core and about 200 bp of DNA are wrapped around the protein complex to form a ...
the last histone, ..., seals off the DNA as it enters and leaves the nucleosome, stabilizing the structure further
H2A; H2B; H3; H4
nucleosome
H1
319
... create more organized and compacted DNA
nucleosomes
320
histones are an example of ... --> proteins that associate with DNA
most others are .. soluble and tend to stimulate processes like transcription
nucleoproteins
| acid
321
during interphase, DNA is ... such that replication is more efficient
small percent of chromatin remains compacted and is therefore transcriptionally silent --> ...: tends to have ... sequences
...: dispersed chromatin that contains genetically active DNA
uncondensed
heterochromatin; highly repetitive
euchromatin
322
DNA replication cannot extend to the ..., or else sequences and info will be lost with each round of replication
solved by a ...: simple repeating unit (TTAGGG) at end of DNA
end of a chromosome; telomere
323
telomeres are progressively shortened but can be replaced with ..., which is more expressed in rapidly dividing cells
telomeres have second function: high ... content creates strong strand attractions at end of chromosomes to prevent ...
telomerase
GC
unraveling
324
...: region of DNA found in center of chromosomes and act as sites of constriction
composed of ... and is made up of repeat sequences that have a high GC content
during cell division, sister chromatids can remain connected at the ... until separated during anaphase
centromeres
heterochromatin
centromere
325
.../...: set of specialized proteins that assist DNA polymerases
replisome; replication complex
326
DNA replication:
| DNA unwinds at ... and generation of new DNA proceeds in ..., creating .... on both sides of the origin
origins of replication; both directions; replication forks
327
... origins of replication in eukaryotes
multiple
328
as replication forks move toward each other and sister chromatids are created, the chromatids remain
connected at the centromere
329
... unwinds DNA in replication
helicase
330
... bind to unraveled DNA 🧬, preventing reassociation of the DNA strands of degradation by nucleases
single-stranded DNA-binding proteins
331
helicase unwinding causes ... -- wrapping of DNA on itself as the helical structure is pushed further toward telomeres during replication
... relive this torsional strain and prevent strand breakage by working ahead of helicase and making small cuts in one/both of the strands and later reseal the cut strands
positive supercoiling; DNA topoisomerases
332
parental strands serve as templates for the generation of new daughter strands --> ... process bc one parental strand is retained and bonded to a new daughter strand
semiconservative
333
DNA polymerase reads the DNA template from ... to ... and synthesizes from ... and ...
3'; 5'; 5'; 3'
334
leading strand is the parental ... strand and is the strand that is copied in a ... fashion
3'; 5'; continuous
335
lagging strand: copied in a direction ...; the parental ... strand
must be copied in small strands called ... DNA polymerase must go back and fill in gaps
opposite the direction of the replication fork; 5' to 3;
| Okazaki fragments
336
dna polymerase cannot make new strands so a ... synthesizes a short ...
these short sequences are constantly being added to the lagging strand bc each Okazaki fragment must start with a new primer
leading strand only requires one in theory (in reality, there are a few)
primase; RNA primer
337
as new phosphodiester bonds are made in dNA, a free ... is released
pyrophosphate (PPi)
338
DNA polymerase .../..., ..., and ... synthesizes daughter strands and RNA primers are then removed by DNA polymerase .../... and replaced by DNA polymerase .../DNA polymerase ...
III; alpha, delta, and epsilon
I/RNAse H
I; delta
339
... seals the ends of the DNA molecules together to create one continuous strand of DNA
DNA ligase
340
bacterial chromosome is closed, double-stranded circular DNA with a ... origin of replication. There are ... replication forks that move away from one another and then eventually meet, resulting in production of two identical ...
single; circular DNA molecules
341
Five "classic" DNA polymerases in eukaryotic cells:
DNA polymerases ..., ..., and... work together to synthesize both the leading and lagging strands: DNA polymerase ... also fills in the gaps left behind when RNA primers are removed
alpha; delta; epsilon
| delta
342
Five "classic" DNA polymerases in eukaryotic cells:
| DNA polymerase ... replicates mitochondrial DNA
gamma
343
Five "classic" DNA polymerases in eukaryotic cells:
| DNA polymerases ... and .... are important to the process of DNA repair
beta; epsilon
344
Five "classic" DNA polymerases in eukaryotic cells:
DNA polymerases ... and ... are assisted by the ... protein, which assembles into a trimer to form the ... -- strengthens the interaction between DNA polymerases and the template strand
delta; epsilon; PCNA; sliding clamp
345
DNA polymerase cannot complete synthesis of 5' end and so chromosome becomes shorter --> fixed by ...
telomeres
346
cancer cells proliferate excessively bc they divide without ... and aren't subject to normal controls on proliferation
can migrate by ... or ... -- migration to distant tissues via bloodstream/lymphatic system
stimulation
| local invasion; metastasis
347
...: mutated genes that cause cancer
| mostly ...-related proteins
oncogenes
| cell cycle
348
oncogens:
...: named after sarcoma; abnormal alleles encode proteins that are more active than normal proteins and promote rapid cell cycle advancement --> mutation in 1 copy is enough to promote tumor growth --> ...
Src; dominant
349
...: oncogenes before they are mutated
| ...: mutated genes that cause cancer that normally would function to stop tumor progression
proto-oncogenes
| antioncogenes
350
antioncogenes:
... or ... are tumor suppressor genes that code for proteins that inhibit the cell cycle/participate in DNA repair
promote cancer by losing their ... activity
...
P53; Rb
tumor suppression
recessive
351
DNA polymerase proofreads DNA strands. mismatched nucleotides tend to be ... and the polymerase can recognize this and fix the error
unstable
352
to differentiate between template and parent strands such that the polymerase knows which nucleotide should actually be there:
parent strand existed longer and tends to be more heavily ...
methylated
353
.... lacks proofreading ability and this is what closes the gaps between Okazaki fragments, not polymerase, so mutations in the ... strand are more likely than for the other strand
DNA ligase; lagging
354
cells have machinery in the ... phase of the cell cycle for mismatch repair (bc this is where the cell checks to ensure that DNA has been replicated properly)
enzymes encoded by genes ... and ... detect and remove errors in replication
... and ... are the genes for prokaryotes
G2
MSH2; MLH1
MutS; MutL
355
UV light induces formation of ..., which interferes with normal gene expression and replication and distorts double helix
removed by ... repair mechanism --> proteins scan DNA and recognize legion. ... makes nicks in the phosphodiester backbone on both sides of the abnormality and removes it. .... fills in the gaps. nick is sealed using ...
```
thymine dimers
nucleotide excision
excision endonuclease
dna polymerase
ligase
```
356
thermal energy can be absorbed by DNA and can lead to ..., which converts cytosine to ...
deamination; uracil
357
...: detection systems that exist for small, non-helix distorting mutations in bases
affected base is recognized and removed by a ..., leaving an .../..., or .., site
base excision repair
glycosylase
apurinic/apyrimidinic; abasic
358
base excision repair contd:
the apurinic/apyrimidinic (AP) site is recognized by an ... that removes the damaged sequence from the DNA and DNA polymerase and ligase fill in gap and seal the strand
AP endonuclease
359
... allows a DNA fragment from any source to be multiplied either by cloning or PCR
means of analyzing and altering genes and proteins
...
... of genetic diseases
...
can provide a source of a specific protein
recombinant DNA tech
genetic testing
prenatal diagnosis
gene therapy
360
DNA cloning:
| Desired DNA is inserted into a ..., forming a ... This is usually a plasmid
vector; recombinant vector
361
DNA cloning contd:
bacteria with recombinant DNA is then ... and the non-recombinant bacteria are killed off with ...
recombinant bacteria must be ...
bacteria can then be left to express the gene or lysed to reisolate that gene depending on what is needed
grown in colonies; antibiotics
| antibiotic resistant
362
insertion of DNA into a plasmid can be facilitated by ... --> enzymes that are bacterial in origin and cleave ... DNA at specific sequences
...: the 5' to 3' sequence of one strand is identical to the 5' to 3' sequence of the antiparallel strand
restriction endonucleases; palindromic
| palindromic
363
some restriction endonucleases yield ... which allow the fragment to be inserted directly into the vector when the vector is cut with the same restriction enzyme
sticky ends
364
...: large collections of known DNA sequences
DNA libraries
365
... contain large fragments of DNA, and include both coding (exon) and noncoding (intron) regions of the genome
genomic libraries
366
... (...) libraries are constructed by reverse transcribing processed mRNA and thus lacks ... --> aka ... libraries
cDNA; complementary DNA; introns; expression
367
only ... can be used to reliably sequence specific genes and identify disease-causing mutations, produce recombinant proteins, or produce transgenic animals
cDNA libraries
368
...: joining of complementary base pair sequence --> DNA-DNA recognition or DNA-RNA recognition
uses two single stranded sequences
part of PCR and southern blotting
hybridization
369
```
PCR: ... DNA
requires ..., ..., and ...
requires ... to denature DNA
uses ..., which doesn't denature under the high temp conditions
amount of DNA is ... each cycle
```
```
amplifies
primers; nucleotides; DNA polymerase
heat
taq polymerase
doubled
```
370
... can be used to separate DNA
| ... is used to separate DNA by size
gel electrophoresis
| agarose gel
371
gel electrophoresis:
| often used while performing a ... - used to detect the presence and quantity of various DNA strands in a sample
southern blot
372
gel electro/southern blot
DNA cut by restriction enzymes and separated by gel electro
DNA fragments transferred to a membrane that is ... with copies of a ... sequence, which binds to its complementary sequence to form double-stranded DNA
probes are labeled with .../... proteins
probed; single-stranded DNA
| radioisotopes; indicator
373
...: contains a hydrogen at both C-3' and 2' --> once incorporated into a dNA strand, polymerase can no longer add to chain
... DNA strands --> useful for DNA sequencing
dideoxyribonucleotides
| terminates
374
...: offers potential cures for inherited diseases; involves transferring a normal copy of a mutated gene into the affected tissues
requires efficient ... --> tend to be modified ...
drawback: randomly integrated DNA poses risk of integrating near and activating a host ...
gene therapy
gene delivery vectors
viruses
oncogene
375
transgenic mice are altered at their ... by introducing a cloned gene into ova or embryonic stem cells
germ line
376
...: introduced cloned gene
transgene
377
transgenic mice:
can be used to study ... from early embryonic development
can be developed by microinjecting a .. into nucleus of newly fertilized ovum such that gene (hopefully, but rarely) incorporates into DNA. this is then implanted in a ... offspring would have transgene and would pass it onto offspring. not as useful for studying ... diseases bc number of copies of the gene that insert into genome cannot be controlled
disease processes
cloned gene
surrogate mother
recessive
378
transgenic mice:
other method: using ... lines --> cloned genes can be introduced in cultures
stem cells injected into ... and implanted into surrogate mothers -- blastocyst has stem cells containing the transgene and the original blastocyst cells that lack the transgene --> offspring will be ...
embryonic stem cell
blastocysts
chimera
379
transgenic mice:
other method contd:
chimeras can be bred to produce mice that are ... for the transgene and ... for the transgene
heterozygous; homozygous
380
...: mice in which a gene has been intentionally deleted to study human diseases
knockout mice
