Test One Flashcards
1
Q
what is a 5’ overhang
A
5’ side has many nucleotides attached
2
Q
where does Z form of DNA exist
A
higher ion concentration
3
Q
why does single stranded DNA or RNA fold on itself
A
stabilizes structure by base complementation
base pairing
4
Q
what are the two types of supercoiling
A
positive and negative
5
Q
restriction enzymes in prokaryotes can recognize
A
cell DNA vs foreign DNA
6
Q
what is a van der waals interaction
A
electron distribution around an atom is asymmetrical
7
Q
delta G= 0
A
initial and final states in equilibrium
8
Q
what type of bond is a phosphodiester bond
A
covalent bond
9
Q
what does polycistronic mean
A
multiple genes are being transcribed into multiple proteins
10
Q
what is the melting temp (Tm)
A
temp in which half of the DNA molecule lost its double helical structure
11
Q
what type of bond is used in the secondary structure to associate adjacent aa
A
hydrogen bonds between O of C=O and H of N-H in peptide bonds
12
Q
what are fatty acids
A
long nonpolar hydrocarbon molecules with a carboxylic group as a polar head
13
Q
what are the characteristics of alpha helix
A
can bend and stretch
14
Q
what aa are hydrophobic
A
gly, ala, leu, ile, val, pro, trp, phe, met
15
Q
what type of bond is the sugar-phosphate bone
A
covalent
16
Q
why is the core of collagen so crowded
A
three helices twisting around each other
17
Q
what type of elements are used in covalent bonds
A
non metals
18
Q
what turn is a omega turn
A
omega turn
19
Q
where can you find proline
A
between different regions of secondary structure within a protein chain
20
Q
third step of DNA synthesis from RNA
A
DNA transcript of viral RNA uses reverse transcriptase to synthesize second strand of DNA creating double helical viral DNA
21
Q
what is the main enzyme needed for DNA replication
A
DNA polymerase
22
Q
RNA transcription direction?
A
5’ to 3’
23
Q
why can cells grow on a medium with antibiotics
A
resistant gene was placed in plasmid and has reporter gene that allows growth on medium
24
Q
what is the reporter gene site in a vector
A
a gene that codes for a protein which tells the researcher that the plasmid arrived successfully inside the cell
25
what is an example of a retrovirus
HIV
26
if the base is C, we call it what with deoxy
deoxycytidine triphosphate
| dCTP
27
deoxyribose has what at 2' carbon
hydrogen
28
hydrophobic aa in rhodospin face
outward
29
what aa contribute to H bonding within protein and substrates
ser, thr, asn, gln
30
what turn is a beta turn
reverse turn or hairpin turn
31
what aa are negatively charge
asp, glu
32
how are the side chains on alpha helix
projected outward
33
negative supercoiling stores free energy that helps
unwind DNA during replication and transcription
34
schematically, what represents an alpha helix
ribbon or cylinder
35
b-form DNA r or L handed helix
R
36
what is transcription
process of copying DNA into RNA by RNA polymerase
37
what aa are neutral-polar
ser, thr, tyr, asn, gln, cys
38
who discovered restriction enzymes
hamilton smith
39
if the base is G, we call it what with ribo
guanosine triphosphate
| GTP
40
what is the correct complement of DNA sequence
| ACCG
CGGT
41
hydrophilic aa in rhodospin face
inward
42
delta G> 0
unfavorable for reaction to occur spontaneously
43
what is another name for super helix
coiled coil
44
which aa is an aliphatic side chain
tyrosine
45
where are bases added to in hyrdroxyl group during DNA synthesis
3'
46
nitrogenous bases has what length of wavelength for uv light
260 nm
47
what type of interaction can form between the R groups of I and M
hydrophobic
48
who created the PCR
Kary Mullins
49
what is an example of tertiary structures
alpha-keratin
50
requirements for RNA polymerization
DNA template, NTP, magnesium ions
51
what kind of bonding is found in water
hydrogen bonding
52
nucleotides
repeats of different monomeric units
53
delta G < 0 endergonic or exergonic?
exergonic
54
Reverse-transcription
process of copying RNA into DNA by reverse transcriptase
55
what type of interaction can form between the R groups of E and K
ionic
| due to each having opposite charges
56
circular DNA can coil on itself and be called?
supercoiled
57
if the base is T, we call it with ribo
thymidinetriphosphate
| TTP
58
is DNA or RNA stronger, why?
DNA bc OH bond is easier to break
59
what is a beta sheet
aggregate of beta strands
60
what enzymes are needed to clone a gene into a plasmid vector
restriction enzyme
| DNA ligase
61
what are cysteine residues in used for in coiled coils
creating di-sulfide bonds to stabilize tertiary structure
62
what are the three features of a vector
origin of replication
multiple cloning site
reporter gene
63
what is a 3' overhang
3' side has many nucleotides attached
64
what are the three different temperatures for PCR
```
DNA denaturation (95)
primer annealing (52-65)
DNA synthesis (72)
```
65
what is splicing
removing introns and putting exons together
66
what kind of curve shows melting temp and denature of DNA
sigmoidal curve
67
the transcription and translation processes in prokaryotes are said to be....
coupled
68
what is the first law of thermodynamics
the total energy of a system and its surroundings is constant
69
what side chain causes hydrophobic
aromatic side chain
70
what attaches to amino acids to make aminoacyl-tRNA
ligases
71
where does b form of DNA exist
higher humidity
72
what type of chromosomes are in eukaryotes
linear
73
with shared electrons in a covalent bond hold what together
atoms together by attracting nuclei of both atoms
74
function of vectors
used to make many copies of gene of interest through replication
also used to express a gene of interest through translation
75
A- form of DNA, R or L helix
R
76
major groove of b form
wide
77
ligases attach to amino acids to make
aminoacyl-tRNA
78
what enzyme is responsible for RNA transcription
RNA polymerase
79
if the base is C, we call it what with ribo
Cytidinetriphosphate
| CTP
80
proteins are what type of polymer of aa
linear
81
what aa is hydroxyproline modified from
proline
82
what sign is total entropy
delta s
83
van der waals is also known as
london dispersion forces
84
as the "properly" folded protein reaches its lowest free energy level the entropy...
increases
85
alpha keratin is found where
hair, wool, hooves, claws and horns
86
what gives the property of aa and function
R group
87
if the base is U, we call it with ribo
uridine triphosphate
| UTP
88
what direction is DNA polymerization (synthesis)
5' to 3'
89
ribonucleotides have what at 2' carbon
OH
90
what is an ionic bond
noncovalent interaction between anion and cation
91
what aa breaks the alpha helix
proline
92
the complementary strand of DNA is
anti-parallel
93
how is a super helix bonded
with weak bonds
94
hydrophobic
water hating
95
what is a hydrogen bond
formed between covalently bound donor hydrogen atom and covalently bound acceptor atom
96
what makes water special
less dense when frozen
excellent solvent
remains liquid in many temps
97
hydrophobic residues in an apolipoprotein face
inward
98
what are the two types of cells in nature
prokaryotes and eukaryotes
99
in aqueous environment, how are proteins built
charged aa are on the surface and hydrophobic aa in the core
100
DNA is composed of
two antiparallel strands hydrogen bonded together
101
what defines cell boundaries and biological reactions
hydrophillic or hydrophobic
102
what aa are hydrophilic
ser, thr, tyr, asn, gln, cys
103
what side is the c-terminal
carboxy terminal
104
minor groove of z form
narrow and extremely deep
105
what is transcription
synthesis of RNA to DNA
106
what is an amphipathic helix
contains both hydrophobic and hydrophilic aa
107
what macromolecule splices DNA
RNA
108
what type of bond connects aa in adjacent beta strands to maintain the structural integrity
h bonds between C=O and N-H
109
what is an example of hydrophobic effect
fatty acids with cell boundaries,
| hydrophobic tail and hydrophilic head
110
restriction enzymes function in nature
cleave foreign DNA molecules
111
tRNA reads what
nucleotide sequence of codon on mRNA
112
base pairs in DNA use what bond
hydrogen bonding
113
what aa can form disulfide bonds
cysteine (2)
114
is rotation restricted in peptide bond
yes
115
what is the function of loops in a secondary structure
important in reversing the direction of the other secondary structure which results in forming a globular compact proteins
116
major groove of A form
narrower and deeper
117
what aa tend to be on inside of protein
hydrophobic aa and aromatic aa
118
what is needed to clone a gene into a plasmid vector
appropriate vector for job
gene of interest
appropriate host
119
what enzyme is used in reverse transcription
reverse transcriptase
120
what is cohesiveness
water molecules interacting with each other due to hydrogen bonding
121
what is the Van der Waals distance
optimum distance of which two atoms being attracted to each other reach
122
if the base is A we call it what with ribo
Adenosine Triphosphate
| ATP
123
besides alpha and beta secondary structures, what is another
loops
124
how can you make a cell competent
using calcium ion
125
what kind of bond is a disulfide bridge
covalent
126
vectors are
genetically engineered plasmids
127
what is the coding region of DNA
transcribed region of DNA
128
what is a consequence of using aa in repeated fashion
helix is stabilized by the pyrrolidine rings of every proline/hydroxyproline avoiding each other/ stearic repulsion
129
what makes up a myoglobin
alpha helices and turns
130
is the hydrogen in hydrogen bonds acceptors or donors
donor
131
what are regulatory sequences
enhancers, promoters, transcription factor binding sites
132
what is the zwitterionic form of aa
when aa is both positive and negative
133
what is the third aa in peptide sequence of collagen
glycine
134
where can you find disulfide bonds
extracellular proteins
135
what water polar or nonpolar
polar
136
function of myoglobin
carry oxygen to muscles
137
do non polar molecules react with water
no
138
as soon as the mRNA is transcribed in prokaryotes, what can happen
ribosomes will attach to it and start translating it
139
Does DNA or RNA absorb more UV light, why?
RNA, due to only one strand so not being blocked
140
what does PCR do
technique to amplify any target sequence (fragment) from the entire DNA molecule
141
the tertiary structure of proteins is at what level of free energy
lowest level
142
what are recombinant DNA technology
manipulating DNA sequences
143
nucleic acids in RNA and DNA carry...
the info for making proteins
144
what are the two important properties of water
polarity and cohesiveness
145
why are D isomers slightly less soluble
tend to form crystals
146
what aa are positively charged
lys, arg, his
147
if the base is T, we call it with deoxy
deoxythymidine triphosphate
| dTTP
148
what are some technique names of manipulating DNA sequences
```
Restriction enzymes
blotting techniques
plasmids and cloning
polymerase chain reaction
DNA sequencing
nucleic acid synthesis
```
149
DNA carries what material
genetic
150
function of porins
outer membrane protein that functions as channel
151
what type of forces are present in covalent bonds
attractions between electron and nuclei
repulsion between electrons
repulsion between nuclei
152
myoglobin is an example of what type of structure
tertiary
153
what makes plasmids useful
can carry extra genes
antibiotic resistance
different enzymes allow host to utilize different food source
pathogenicity-related genes
154
what is the core structure of alpha keratin
two alpha helices twist around each other to form super helix
155
manipulating DNA sequences entails
```
cutting it to specific fragments
extracting sequences that encode genes or regulatory sequences
expressing specific genes in organisms
cloning
sequencing
```
156
the amino acid attachment site binds to the
3' or 2' hydroxyl group of the 3' end of the tRNA
157
where is energy acquired from
surroundings
158
what is the template recognition site
contains anticodon which is annealed to mRNA
159
what type of chromosomes are in prokaryotes
circular
160
what enzyme is used for DNA replication from RNA
reverse transcriptase
161
primary structure
description of linear aa sequence of polypeptide
162
what is the distance between repeating units in an alpha helix
5.4 A
163
what was the first discovered secondary structure
alpha helix
164
what was the first protein sequence
insulin
165
what is the henderson hasselbalch equation
pH=pKa+log (conj base/acid)
166
if pH>pka then
chemical group is not protonated
167
if order for delta G to be negative then
delta s of universe has to increase
168
where does A form DNA exist
lower humidity
169
translation
ribosome-mediated production of a polypeptide whose amino acid sequence is specified by the nucleotide sequence in an mRNA
170
how is the alpha helix stabilized
h bonds between C=O group of aa and N-H group of aa situated three residues ahead
171
if single strand DNA or RNA fold on themselves what structure does it create
secondary
172
base stacking uses what type of bonding
van der waals bonding, sharing of pi electrons between base pairs
173
who discovered the alpha helix in the secondary structure
pauling, corey, branson
174
besides R group what other part of aa do you have to worry about charge
amino terminal and carboxy terminal
175
coiled coils have an imperfect repeat of how many aa
7
176
pyrimidine
cytosine, thymine, uracil
177
why can glycine fit in tight places
small aa, with no side chain
178
what is the multiple cloning sites in a vector
where "foreign" DNA is inserted
179
what bond is the strongest bond
covalent bonds
180
what is needed for transformation
restriction digest/ pcr
ligation into a plasmid
transformation into competent cells
further analysis
181
how many cycles can a PCR run
25-35
182
how many bp/turn in Z form
12
183
what does monocistronic mean
only one gene being coded into one protein
184
if the base is G, we call it what with deoxy
deoxyguanosine triphosphate
| dGTP
185
what dictates the secondary, tertiary and quaternary structure of proteins
primary structure
186
what are the three parts of an amino acid
amine group
side chain
carboxyl group
187
how do the side chains sit to the plane of the sheet in a beta sheet
perpendicular
188
what is a tertiary structure
the association of the secondary structure elements with one another which give the polypeptide its overall structure
189
messenger RNA is
the template for protein synthesis
190
is hydrophobic effect a bond
no, just a mean to minimize chaos in presence of water
191
what is an intron
non genetic area of DNA
192
what is in the protein backbone
amino acids joined by peptide bonds
193
purines
adenine, guanine
194
what is transformation with plasmid
the process by which a host organism can take up DNA from environment
195
secondary structure
the association of the adjacent aa within the primary structure with one another
196
why are polar molecules easily soluble in water
the more electronegative atom wants to accept the donor hydrogen to create a hydrogen bond
197
surroundings refers to
the matter in the rest of the universe
198
what is a promoter
sites on DNA molecules that signal RNA polymerase that there is a gene ahead
199
what is a liposome
bilayer with hydrophilic core
200
what is the origin of replication in a vector
regulatory sequence where replication is initiated
201
DNA topology has to do with
coiling of DNA or RNA strand
202
so any energy released in the formation of a chemical bond must be used to
break another bond
released as heat
stored in other form
203
Tobacco Mosiac Virus (TMV) replicates its RNA genome using what enzyme
RNA-directed RNA polymerase
204
hydrophillic
water loving
205
what type of single strands are messenger RNA
irregular
206
where is deoxyribose linked to with a phosphate group
5' carbon
207
why does eukaryotes have a more complicated version of mRNA
must be processed before protein synthesis
208
what is an apolipoprotein
alpha helix that has both hydrophilic and phobic aa
209
what type of proteins represent an amphipathic alpha helix
apolipoprotein and rhodopsin
210
how many bp/turn in b form
10
211
the backbone of DNA is made of
sugar-phosphate repeats
212
delta G> 0 endergonic or exergonic?
endergonic
213
what modified aa does collagen use
hydroxyproline
214
more s-s bridges means
less flexibility and more strength
215
what side is the n- terminal
amino terminal
216
Z form DNA R or L handed helix
L
217
what makes DNA sequence so specific to restriction enzymes
dna fignerprint
218
the area on DNA before the transcribed region is called
regulatory DNA sequences, promoter region
219
why is glycine used in collagen
small aa it can fit into three helix
220
what is pKa
the pH at which the protonated and unprotonated species are equal
221
if the base is U, we call it with deoxy
deoxyuridine triphosphate
| dUTP
222
what aa are neutral- nonpolar
gly, ala, leu, ile, val, pro, trp, phe, met
223
tRNA is the adapter molecule between....
nucleotide sequence and amino acid sequence
224
what bond angles can rotate
phi and psi
| bond within one aa
225
what is gene expression
overall process by which the information encoded in a gene is converted into a phenotype
226
in bacteria how many enzymes required for DNA replication
20
227
why is "complementary" used in van der waals interaction
two atoms getting closer causes fluctuations in electron distribution which allows the attraction between the two atoms
228
what is annealing
separate strands of DNA from two different organisms and you anneal one strand from an organism to another strand of a different organism
229
how to find free energy
heat from system to surrounding -T(total entropy of sys)
230
which aa can switch from + to no charge due to environment
histidine
231
genes in prokaryote are...
continuous with no interruptions
232
what is an example of a quaternary structure
collagen
233
the carboxyl group of the aa is .... to 3' hydroxyl group of the 3' end of tRNA
esterfied
234
how are proteins built in porins
charged aa in the core and hydrophobic aa on surface
235
how to find number of DNA replicas in PCR
2^n
| n= number of cycles
236
what are micelles
round groups of fatty acids, with polar head facing water and nonpolar tails not facing water in center
237
what is the helper group of myoglobin
heme
238
what is the central dogma
DNA replicating or going to RNA by transcription, then RNA going to Protein due to translation
239
delta G < 0
favorable for reactions to occur spontaneoulsy
240
what is the hydrophobic effect
nonpolar molecules have to aggregate together to lessen the surface area that water touches
241
what does RNA polymerization not require
primer or mechanism to correct wrong bases
242
which aa is an imino acid
proline
243
ribosomal RNA is comprised of what % in cellular RNA
85
244
what does PCR require
DNA template
thermostable DNA polymerase
pair of primers complementing the flanking sequences of the target
245
Messenger RNA is comprised of what % in cellular RNA
around 5
246
who discovered the insulin protein sequence
frederick sanger
247
if the base is A we call it what with deoxy
deoxyadnisone triphosphate
| dATP
248
when are liposomes used
for drugs to reach inside cells without being disrupted by water
249
where are the nitrogenous bases attached to on the deoxyribose
1' of carbon
250
what is hyperchromism
heating DNA, so two strands gradually separate from one another
251
what kind of bond is between carboxyl group of one aa to amino group of another aa
amide bonds/ peptide bonds
252
what type of molecules have covalent bonds
amino acids, carbohydrates, nitrogenous bases, accessory molecules
253
what stabilized the collage three helices
hydrophobic interactions b/w proline and hydroxyproline residues
254
hydrophilic residues in an apolipoprotein face
outward
255
what is required for polymerization of DNA
DNA template
primer
mechanism to correct errors due to replication
dNTP and magnesium ions
256
second law of thermodynamics
the total entropy of a system and its surroundings always increases
257
covalent bonds
electrons being shared between atoms
258
what happens is if the two atoms get too close and is a shorter distance that the van der waals distance
the atoms repulse each other
259
what sign is free energy
delta G
260
what is a palindrome
a word or sentence that reads the same from left to right as does right to left
261
how many aa
20
262
second step of DNA synthesis from RNA
DNA-RNA hybrid uses reverse transcriptase to digest RNA
263
how do you get the total entropy of the surrounding
-(amount of heat from system/temp)
264
What is DNA replication
a process by which DNA molecule duplicates
265
what is total entropy
measure of randomness
266
negative covalent bond
both atoms have similar electronegativity
267
what is an exon
genetic area of DNA
268
which aa is an aromatic side chain
phenylalanine, tyrosine, tryptophan
269
what forms can energy take
kinetic, heat and potential
270
transfer RNA comprises what % of cellular RNA
15
271
what enzymes can denature DNA at physiological temps
helicases
272
knowing the aa sequence of proteins helps us...
predict structure
predict function
molecular pathology
273
minor groove of b form
narrow
274
in water what is the partial charge of hydrogen and oxygen
hydrogen is positive
| oxygen is negative
275
what is the core of myoglobin and surface
core: hydrophobic aa
surface: charged aa
276
major groove of z form
flattened
277
where do plasmids replicate
inside the host cell independently
278
how can beta sheets run
antiparallel and parallel
279
how many bp/turn in A form
11
280
why use a calcium ion to make a cell competent
shields the negative charge of DNA
281
why are ser, thr, asn, and gln contibute to H bonding within protein and with substrates
due to hydroxyl groups and carboxymide groups
282
what are some examples of loops
beta- turn
| omega- turn
283
first step of DNA synthesis from RNA
viral RNA uses reverse transcriptase to synthesize DNA complimentary to RNA
284
in order for reaction to occur spontaneously total entropy must
increase
285
what are cohesive (sticky) ends
asymmetric cleavage of the phosphodiester backbone on both DNA strands
286
what enzyme is used in transcription
RNA polymerase
287
in a single beta strand are there H bonds
no
288
always read DNA
5' to 3'
289
positive supercoiling stores free energy that helps
prevent DNA from unwinding in thermophiles
290
system refers to
matter confined to a definite region of space
291
what are hairpin loops
when ssDNA or RNA folds on each other and the bases pair up with each other from same strand
292
do ions exist as free entities
no they are surrounded by hydration shells
293
if ph< pka then
chemical group is protonated
294
what is a blunt end
both 3' and 5' side have same amount of nucleotide when cleaved by restriction enzyme
295
what sites do restriction enzymes recognize
palindromes
296
what are restriction enzymes
special enzymes that recognized specific DNA sequences and hydrolyze the phosphodiester bond at these sites
297
fatty acids in water demonstrates thermodynamics how
fatty acids aggregate together and order themselves, but overall randomness and chaos of molecules of surrounding is increasing
298
which aa are sole contributors to overall charge of proteins
basic and acidic amino acids
| hydrophilic
299
what is the Tm in which half DNA is in single strand form
85 degrees celsius
300
what makes up collagen
three helices wound around each other
301
where is collagen found
skin, bones, teeth, cartilage, tendons, and blood vessels
302
polar covalent bond
one atom is more electronegative than the other
303
how do restriction enzymes get their names
derived from the organism its extracted from
304
can tyrosine be hydrophilic, why
because OH attached will allow it to be if forced
305
in nature, aa are in what configuration
L isomer
306
what is the function of annealing
to determine organism relatedness
307
minor groove of A form
broader and shallower
308
steps in PCR
DNA heated to denature strands
annealing: DNA strands are cooled to allow them to anneal with primers
Extension: DNA polymerase completes the DNA strand
309
what does an organism being naturally competent mean
can take up DNA from the environment without any intervention
310
in biological systems, energy is related to
the possibility of different molecules to react with one another
311
how many aa residues in a beta strand
8 to 10
312
each turn of an alpha helix is how many aa
3.6
313
in transconfiguration of peptide bond, is it rigid and ....
yes and planar
314
what are zwitterions
aa in cells existing as dipolar ions
315
what do the imperfect repeat of aa in coiled coils do
allow complementary aa to meet at the crossing points, usually hydrophobic aa
