Biochem Test 1 Flashcards
1
Q
A
2
Q
nucleoside
A
contains a ribose or deoxyribose + a nitrogen containing base
3
Q
beta
A
if the base is upward
4
Q
nucleotide
A
nucleoside + a phosphate group
5
Q
purine bases
A
adenine, guanine
6
Q
purine nucleosides
A
adenosine, guanosine
7
Q
pyrimidines
A
cytosine, uracil, thymine
8
Q
pyrimidine nucleosides
A
cytidine, uridine, thymidine
9
Q
in DNA adenine pairs with
A
thymine
10
Q
in DNA guanine pairs with
A
cytosine
11
Q
in RNA thymine pairs with
A
uracil
12
Q
polynucleotides make up
A
nucleic acids
13
Q
polynucleotides are linked through 3’-5’
A
phosphodiester bonds
14
Q
the backbone of nucleic acids are
A
pentose phosphate backbone
15
Q
bases are linked through
A
hydrogen bonding
16
Q
A & T are WEAKER because they only have __ hydrogen bonds where as G & C have _____ hydrogen bonds
A
2, 3
17
Q
____ or ________ can be used as antiviral and cancer drugs
A
nucleoside, base analogues
18
Q
how do analogues work as drugs for cancer or virus
A
they block DNA replication and the virus will be unable to multiply
19
Q
ATP contains 2 ________ that can be hydrolyzed to produce energy for coupled biochemical or cellular processes
A
high-energy phosphate bonds
20
Q
one step energy release for ATP =
A
ADP + Pi
21
Q
two step energy release for ATP =
A
AMP + Pi & PPi = 2Pi
22
Q
UTP
A
combining sugars - constantly used
23
Q
CTP
A
lipid synthesis
24
Q
GTP
A
protein synthesis
25
\_\_\_ ____ & _____ are all energetically equivalent to ATP but specific for different metabolic pathways
UTP GTP CTP
26
ATP + UDP =
ADP + UTP
27
ADP + ADP =
ATP + AMP
28
cellular ATP is main generated through ____ & \_\_\_\_\_
substrate level phosphorylation, oxidative phosphorylation
29
ATP that is generated via ATP generating reactions
substrate level phosphorylation
30
ATP that is generated via electron transport chain
oxidative phosphorylation
31
GTP cycle is associated with changes in ____ & \_\_\_\_
protein conformation & activity
32
cAMP
important second messenger in cell signaling
33
\_\_\_\_\_ inhibitors blocks the degradation of cAMP
phosphodiesterase
34
NAD
Nicotinamide adenine dinucleotide
35
NADP
Nicotinamide adenine dinucleotide phosphate
36
carbohydrates
polyhydroxy aldehydes and ketones
37
functions of carbohydrates
fuels, regulation, structural components
38
caloric contents
the ability of a specific carbohydrate to produce energy
39
carbohydrates caloric content
4 kcal/g
40
fat caloric content
9 kcal/g
41
protein caloric content
4 kcal/g
42
carbohydrates
made of glycogen, present in muscle and liver, store energy for emergency use
43
glyceraldehyde
a triose - a sugar that contains only three carbon atoms
44
a glyceraldehyde is
the simplest carbon with only one chiral carbon
45
D orientation
hydroxyl is on the right
46
L orientation
hydroxyl is on the left
47
enantiomers
are mirror image compounds
48
glucose and most other sugars in human tissues have the ___ configuration
D
49
stereoisomers
the same chemical formula but different 3-D orientation
50
Epimers
stereoisomers that different in the configuration of only chiral center
51
pyranose
6 membered ring with oxygen, D orientation, glucose mostly exists in this form
52
furanose
5 membered ring with oxygen, D orientation
53
anomers
two forms of the same structure (i.e. cyclic)
54
CH2OH same side is
Beta
55
CH2OH opposite side
alpha
56
mutarotation
conversion between anomers
57
Oxidized Sugars
add drug to make it easier to be metabolized & kidney function
58
glucuronidation
addition of glucuronate to a substrate
59
di & polysaccharides consists of monsaccharides linked through \_\_\_\_\_\_
O-glycosidic bonds
60
amylose
alpha 1,4
61
amylopectin
alpha 1,4 & alpha 1,6
62
cellulose
linear Beta 1,4
63
glycogen
structure resembles amylopectin - both alpha 1,4 and alpha 1,6
64
maltose
glucose + glucose alpha 1,4
65
Sucrose
fructose + glucose
66
alpha-amylase
endoglucosidase that specifically cleaves the alpha 1,4 glycosidic bond
67
Na dependent glucose transporters
secondary active transporter
68
facilitating glucose transporters
the GLUT transport protein
69
GLUT 1
RBC & Barriers - high affinity
70
GLUT 2
organs take leftovers - low affinity
71
GLUT 4
sucks up glucose from blood and relies on insulin; reduces blood glucose levels
72
GLUT 4
increases absorption of glucose into the muscle
73
carbohydrates
polyhydroxy aldehydes and ketones
74
functions of carbohydrates
fuels, regulation, structural components
75
caloric contents
the ability of a specific carbohydrate to produce energy
76
carbohydrates caloric content
4 kcal/g
77
fat caloric content
9 kcal/g
78
protein caloric content
4 kcal/g
79
carbohydrates
made of glycogen, present in muscle and liver, store energy for emergency use
80
glyceraldehyde
a triose - a sugar that contains only three carbon atoms
81
a glyceraldehyde is
the simplest carbon with only one chiral carbon
82
D orientation
hydroxyl is on the right
83
L orientation
hydroxyl is on the left
84
enantiomers
are mirror image compounds
85
glucose and most other sugars in human tissues have the ___ configuration
D
86
stereoisomers
the same chemical formula but different 3-D orientation
87
Epimers
stereoisomers that different in the configuration of only chiral center
88
pyranose
6 membered ring with oxygen, D orientation, glucose mostly exists in this form
89
GLUT 4
increases absorption of glucose into the muscle
90
GLUT 4
sucks up glucose from blood and relies on insulin; reduces blood glucose levels
91
GLUT 2
organs take leftovers - low affinity
92
GLUT 1
RBC & Barriers - high affinity
93
facilitating glucose transporters
the GLUT transport protein
94
Na dependent glucose transporters
secondary active transporter
95
alpha-amylase
endoglucosidase that specifically cleaves the alpha 1,4 glycosidic bond
96
Sucrose
fructose + glucose
97
maltose
glucose + glucose alpha 1,4
98
furanose
5 membered ring with oxygen, D orientation
99
glycogen
structure resembles amylopectin - both alpha 1,4 and alpha 1,6
100
cellulose
linear Beta 1,4
101
amylopectin
alpha 1,4 & alpha 1,6
102
amylose
alpha 1,4
103
di & polysaccharides consists of monsaccharides linked through \_\_\_\_\_\_
O-glycosidic bonds
104
glucuronidation
addition of glucuronate to a substrate
105
Oxidized Sugars
add drug to make it easier to be metabolized & kidney function
106
mutarotation
conversion between anomers
107
CH2OH opposite side
alpha
108
CH2OH same side is
Beta
109
anomers
two forms of the same structure (i.e. cyclic)
110
all naturally occurring fatty acids are in ___ formation
cis
111
w counts
backwards
112
#:#
carbons:number of double bond
113
transfat
not naturally, bad for cholesterol, trans confirmation
114
Melting point increases
with chain length
115
Melting point decreases
when number of bonds increase
116
saturated
no double bonds
117
unsaturated
contains double bonds
118
triacylglyerols
stereospecific; chiral
119
unsaturated fats preferable form ester bonds with the ___ carbon of glycerol
C2
120
the N+ makes the molecule
hydrophilic
121
the head of the phospholipid is
hydrophillic
122
the tail of the phospholipid
hydrophobic
123
all head groups attach to the ____ on phospholipids
the phosphate group
124
the phosphate group is
hydrophilic
125
the phosphate group is attached to the in phosphocylglycerols
C3
126
phospholipids
lipid on a membrane, contains a phosphate
127
phosphoacylglycerols
have the phosphate on C3
128
phospholipase A1
cuts after the oxygen on C1
129
phospholipase A2
cuts after the oxygen on C2
130
phospholipase C
cuts between the oxygen and phosphate leaving the head group and phosphate
131
phospholipase D
cuts the head group off along with the oxygen
132
shingolipids
sugars or a head group is added to the hydroxyl group of ceramics to form various sphingolipids
133
phosphoshingolipids
attached to a phosphate
134
steroids
very hydrophobic with a 1 hydrophilic -OH group
135
amino acids contain
an amino group, alpha carbon, carboxylic acid and side chain
136
amino acids are building blocks for ___ and \_\_\_\_\_
peptides & proteins
137
all amino acids in mammals have the ___ configuration
L
138
higher ka = _____ pka = \_\_\_\_\_\_
lower , more easily deprotonated
139
Ka
dissociation constant
140
pH
-log[H+]
141
pKa
-logKa
142
ka
[H+][A-]/[HA]
143
pka (practical definition)
the pH at which half of an acid or conjugate acid is deprotonated
144
at physiological pH free amino acids exist largely as \_\_\_\_\_
zwitterions
145
the structural and fuctional diversity of proteins is ultimately defined by the structural diversity of amino acid \_\_\_\_\_
side chain
146
non polar aliphatic amino acids
have non-aromatic hydrocarbon side chains
147
which has a kink in the backbone
proline
148
what is the pka for a carboxyl
2
149
what is the pka for an amino
10
150
higher hydropathy index means
more hydrophobic (typically more bulky)
151
hydrophobic side chains are responsible for the ______ which is defined as the observed tendency of hydrophobic groups to cluster together in aqueous environment
hydrophobic effect
152
arginine side chain has a
guanidinium group
153
histidine side chain contain an
imidazole ring
154
which is the major charge contributor of a long peptide or protein
side chain
155
the charge of amino acid depends on \_\_\_\_
its environment
156
isoelectric point
is defined as the pH at which the net charge of a molecule in a solution equals to zero; is a characteristic of a specific amino acid or a protein and does not depend on the chemical environment around the molecule
157
disulfide bonds are responsible for
maintaining structural integrity of proteins and peptides
158
cystinuria
caused by a genetic defect in a transporter involved in amino acid reabsorption; has low solubility and precipitate in the urine to form kidney stones
159
essential amino acids
nine amino acids are essential in the diet of human adults
160
essential amino acids
nine amino acids are essential in the diet of human adults
161
cystinuria
caused by a genetic defect in a transporter involved in amino acid reabsorption; has low solubility and precipitate in the urine to form kidney stones
162
disulfide bonds are responsible for
maintaining structural integrity of proteins and peptides
163
isoelectric point
is defined as the pH at which the net charge of a molecule in a solution equals to zero; is a characteristic of a specific amino acid or a protein and does not depend on the chemical environment around the molecule
164
the charge of amino acid depends on \_\_\_\_
its environment
165
which is the major charge contributor of a long peptide or protein
side chain
166
histidine side chain contain an
imidazole ring
167
arginine side chain has a
guanidinium group
168
hydrophobic side chains are responsible for the ______ which is defined as the observed tendency of hydrophobic groups to cluster together in aqueous environment
hydrophobic effect
169
higher hydropathy index means
more hydrophobic (typically more bulky)
170
what is the pka for an amino
10
171
what is the pka for a carboxyl
2
172
which has a kink in the backbone
proline
173
non polar aliphatic amino acids
have non-aromatic hydrocarbon side chains
174
the structural and fuctional diversity of proteins is ultimately defined by the structural diversity of amino acid \_\_\_\_\_
side chain
175
at physiological pH free amino acids exist largely as \_\_\_\_\_
zwitterions
176
pka (practical definition)
the pH at which half of an acid or conjugate acid is deprotonated
177
ka
[H+][A-]/[HA]
178
pKa
-logKa
179
pH
-log[H+]
180
Ka
dissociation constant
181
higher ka = _____ pka = \_\_\_\_\_\_
lower , more easily deprotonated
182
all amino acids in mammals have the ___ configuration
L
183
amino acids are building blocks for ___ and \_\_\_\_\_
peptides & proteins
184
amino acids contain
an amino group, alpha carbon, carboxylic acid and side chain
185
messenger RNA
template for protein synthesis
186
transfer RNA
carries amino acids to growing peptide
187
ribosomal RNA
RNA component of ribosome (protein synthesis)
188
heat duration
breaks hydrogen bonds
189
melting temperature
at which half of DNA is denatured
190
annealing or renaturation
gradually cooling
191
enzyme known as _____ ca relieve the stress caused by supercoiling to allow DNA unwinding
toposiomersases
192
nucleosomes
nucleosome core + DNA + histone H1
193
solenoid structure
nucleosomes wind into helical tubular coils
194
nonhistone chromosomal proteins
enzymes acting on DNA and transcriptional factors also associate with DNA
195
why do we package our DNA
protection regulations
196
genetic
the fundamental unit of heredity
197
structural definition
encompasses the DNA sequence that encodes the structural components of the gene product together with its 5' end adjacent regulatory region
198
genetic locus
a specific location on a chromosome
199
allele
alternative versions of the same gene in a diploid
200
homozygous
having two identical alleles in a dipoloid
201
heterozygous
having two different alleles in adiploid
202
dominant trait
an inherited characteristic that appears in a diploid offspring if only one copy of the corresponding allele is present. the trait of the other allele is know as recessive
203
intron
non-coding genomic sequence within a gene
204
exon
coding genomic sequence within a gene
205
double helix
single stranded; intra-chain base pairing to form loop structures for binding to proteins or other regions of RNA
206
mRNA
provides template
207
codon
a sequence of three nucleotide that together form a unit of genetic code in a DNA or RNA molecule
208
prokaryotic ribosomes
70s
209
eukaryotic cytoplasmic ribosomes
80s
210
mitochondrial ribosomes
55s
211
peptide transferase
form peptide bond inside ribosome
212
oligoribonucleotides
serve as primers during DNA replication
213
small nuclear ribonucleoprotiens
are involved in mRNA maturation
214
microRNAs
participate in regulation of gene expression
215
heterozygous
having two different alleles in adiploid
216
dominant trait
an inherited characteristic that appears in a diploid offspring if only one copy of the corresponding allele is present. the trait of the other allele is know as recessive
217
intron
non-coding genomic sequence within a gene
218
exon
coding genomic sequence within a gene
219
double helix
single stranded; intra-chain base pairing to form loop structures for binding to proteins or other regions of RNA
220
mRNA
provides template
221
codon
a sequence of three nucleotide that together form a unit of genetic code in a DNA or RNA molecule
222
prokaryotic ribosomes
70s
223
eukaryotic cytoplasmic ribosomes
80s
224
mitochondrial ribosomes
55s
225
peptide transferase
form peptide bond inside ribosome
226
oligoribonucleotides
serve as primers during DNA replication
227
small nuclear ribonucleoprotiens
are involved in mRNA maturation
228
microRNAs
participate in regulation of gene expression
229
ribosomal RNA
RNA component of ribosome (protein synthesis)
230
heat duration
breaks hydrogen bonds
231
melting temperature
at which half of DNA is denatured
232
annealing or renaturation
gradually cooling
233
enzyme known as _____ ca relieve the stress caused by supercoiling to allow DNA unwinding
toposiomersases
234
nucleosomes
nucleosome core + DNA + histone H1
235
solenoid structure
nucleosomes wind into helical tubular coils
236
nonhistone chromosomal proteins
enzymes acting on DNA and transcriptional factors also associate with DNA
237
why do we package our DNA
protection regulations
238
genetic
the fundamental unit of heredity
239
structural definition
encompasses the DNA sequence that encodes the structural components of the gene product together with its 5' end adjacent regulatory region
240
genetic locus
a specific location on a chromosome
241
microRNAs
participate in regulation of gene expression
242
small nuclear ribonucleoprotiens
are involved in mRNA maturation
243
oligoribonucleotides
serve as primers during DNA replication
244
peptide transferase
form peptide bond inside ribosome
245
mitochondrial ribosomes
55s
246
eukaryotic cytoplasmic ribosomes
80s
247
prokaryotic ribosomes
70s
248
codon
a sequence of three nucleotide that together form a unit of genetic code in a DNA or RNA molecule
249
mRNA
provides template
250
double helix
single stranded; intra-chain base pairing to form loop structures for binding to proteins or other regions of RNA
251
exon
coding genomic sequence within a gene
252
intron
non-coding genomic sequence within a gene
253
dominant trait
an inherited characteristic that appears in a diploid offspring if only one copy of the corresponding allele is present. the trait of the other allele is know as recessive
254
heterozygous
having two different alleles in adiploid
255
homozygous
having two identical alleles in a dipoloid
256
allele
alternative versions of the same gene in a diploid
257
transfer RNA
carries amino acids to growing peptide
258
transfer RNA
carries amino acids to growing peptide
259
ribosomal RNA
RNA component of ribosome (protein synthesis)
260
heat duration
breaks hydrogen bonds
261
melting temperature
at which half of DNA is denatured
262
annealing or renaturation
gradually cooling
263
enzyme known as _____ ca relieve the stress caused by supercoiling to allow DNA unwinding
toposiomersases
264
nucleosomes
nucleosome core + DNA + histone H1
265
solenoid structure
nucleosomes wind into helical tubular coils
266
nonhistone chromosomal proteins
enzymes acting on DNA and transcriptional factors also associate with DNA
267
why do we package our DNA
protection regulations
268
microRNAs
participate in regulation of gene expression
269
small nuclear ribonucleoprotiens
are involved in mRNA maturation
270
oligoribonucleotides
serve as primers during DNA replication
271
peptide transferase
form peptide bond inside ribosome
272
mitochondrial ribosomes
55s
273
eukaryotic cytoplasmic ribosomes
80s
274
prokaryotic ribosomes
70s
275
codon
a sequence of three nucleotide that together form a unit of genetic code in a DNA or RNA molecule
276
mRNA
provides template
277
double helix
single stranded; intra-chain base pairing to form loop structures for binding to proteins or other regions of RNA
278
exon
coding genomic sequence within a gene
279
intron
non-coding genomic sequence within a gene
280
dominant trait
an inherited characteristic that appears in a diploid offspring if only one copy of the corresponding allele is present. the trait of the other allele is know as recessive
281
heterozygous
having two different alleles in adiploid
282
homozygous
having two identical alleles in a dipoloid
283
allele
alternative versions of the same gene in a diploid
284
genetic locus
a specific location on a chromosome
285
structural definition
encompasses the DNA sequence that encodes the structural components of the gene product together with its 5' end adjacent regulatory region
286
genetic
the fundamental unit of heredity
287
messenger RNA
template for protein synthesis
288
messenger RNA
template for protein synthesis
289
homozygous
having two identical alleles in a dipoloid
290
allele
alternative versions of the same gene in a diploid
291
genetic locus
a specific location on a chromosome
292
structural definition
encompasses the DNA sequence that encodes the structural components of the gene product together with its 5' end adjacent regulatory region
293
genetic
the fundamental unit of heredity
294
why do we package our DNA
protection regulations
295
nonhistone chromosomal proteins
enzymes acting on DNA and transcriptional factors also associate with DNA
296
solenoid structure
nucleosomes wind into helical tubular coils
297
nucleosomes
nucleosome core + DNA + histone H1
298
enzyme known as _____ ca relieve the stress caused by supercoiling to allow DNA unwinding
toposiomersases
299
annealing or renaturation
gradually cooling
300
melting temperature
at which half of DNA is denatured
301
heat duration
breaks hydrogen bonds
302
ribosomal RNA
RNA component of ribosome (protein synthesis)
303
transfer RNA
carries amino acids to growing peptide
304
messenger RNA
template for protein synthesis
305
peptide bond
has double bond character; does not allow for rotation
306
which form cis/trans is more favorable for amino acids
trans
307
primary structure
the amino acid sequence; overall conformation
308
conservative mutation
protein structure is not that different; (ie same charge & similar side chains)
309
non-conservative mutation
large difference in side chains (can cause disease)
310
polymorphisms
changes in primary structure that may slightly change function (generally tolerable & not disease causing)
311
tissue specific isoforms
a protein that has a similar structure and function as another but come from different genes
312
species specific variations
insulin (pig cow) or antibodies (mice)
313
developmental variations
fetal hemoglobin with higher affinity than adult hemoglobin
314
secondary structures
localized regions or segments of the peptide chain that fold into specific patterns that are stabilized by intramolecular forces such as hydrogen bonding
315
alpha helix
a rod like structure in which a tightly coiled backbone forms the inner part and the R groups extend outward into a helical array
316
in a helices where does the hydrogen bonding occur
4 apart
317
how is a helices oriented
clockwise, from n terminus top; spiraling; tightly compacted; rod like with R groups pointed outward
318
which AA are referred to as "helix breakers"
proline and glycine
319
Beta pleated sheets
more spread out; hydrogen bonding in parallel or antiparallel fashion; made up of 2 or more beta strands
320
non repetitive secondary structures include
beta hooks (4) and omega loops (10ish) that connect alpha & beta or 2 of the same
321
motifs
small arrangements of secondary structures that are observed in many different proteins; allow for interactions; contain basic amino acids held in place by larger parts of the protein.
322
tertiary structure
the overall folding pattern; interior is hydrophobic while exterior is hydrophilic;
323
what types of bonding occurs in tertiary structure
hydrogen; salt bridges between charged side chains; van Der walls; ring stacking; disulfide bonds
324
Quaternary structure
assembly of multiple individual polypeptide chains into a geometrically and stoichiometric manner
325
2 identical subunits
homodimer
326
3 distinct subunits
heterotrimer
327
domain
can stand alone; superfamily of structures; umbrella containing motifs
328
different types of protein denaturation
heat/high temperature; low or high pH; alcohol; hydrophobic molecules/surfactants; chaotropic agents; heavy metals
329
what is the primary determinate of 3D structure
sequence of amino acids
330
chaperonins
stablize to make it fold correctly; help it get enough energy to go to its native state
331
native confirmation
low energy state
332
cis-trans isomerase
change the conformation of proline by making it cis so it can have hair pin turns
333
disulfide isomerase
breaks bond then the bond reform after proper folding has occurred
334
prion proteins
normal proteins found in the human body; a helix is the most dominant form
335
alzheimers
small petite fragment; gain of toxicity; neuronal degeneration; huge plaques form
336
cystic fibrosis
loss of function; can't get CFTR into the cell membranes; phenylalanine is deleted
