Biochemistry Flashcards
(288 cards)
1
Q
Purines
A
Adenine & Guanine
2
Q
Pyrimidines
A
Cytosine & Thymine
3
Q
Topoisomerase I
A
Cleaves 1 strand of DNA to change topology
Inhibited by Campothecin
4
Q
Topoisomerase II
A
Cleaves both strands of DNA to change topology and relives positive supercoiling during replication
Inhibited by m-AMSA and Doxorubicin
5
Q
Pseudogene
A
Sequences that resemble functional genes but no longer code for normal gene products
6
Q
Processed pseudogene
A
Sequence of DNA that does not code for normal gene products, which likely arose from being reverse transcribed from RNA and incorporated into genomic DNA
7
Q
Proviruses
A
Copies of retroviruses inserted into chromosomes
~8% of human genome derived from retroviruses
8
Q
SINEs
A
Short, interspersed repeat elements
<500 bases
i.e. Alu repeats, ~10% of human genome
9
Q
LINEs
A
Long interspersed repeat elements
>500 bp, constitute ~20% of genome
Complete LINEs encode a reverse transcriptase
10
Q
Microsatellites
A
Arrays of 2-5bp nucleotide repeats, with a mean array size of 100 repeats; highly polymorphic
11
Q
Minisatellites
A
10-50bp nucleotide repeats, present in tandem arrays extending from less than 10 to more than 100
12
Q
Satellite sequence
A
Highly repetitive, short DNA sequences that form large clusters in chromosomes; size of repeat units varies greatly (5-100bp)
13
Q
Nucleosome
A
Complex of 147bp of DNA with histone octamer (two each of H2A, H2B, H3, and H4); basic unit of chromatin fibers utilized to pack DNA more tightly
14
Q
Origin of replication
A
Initiation site for DNA replication
15
Q
Bloom’s syndrome
A
Deficiency of DNA helicase, associated with development of cancer
16
Q
Werner’s syndrome
A
Premature aging disease caused by a defective helicase
17
Q
SV40
A
Simian Virus 40, encodes for T-ag, which binds to SV40 origin and serves as DNA helicase; recruits proteins from host cells to replicate
18
Q
Pol α primase
A
Initiates DNA synthesis by binding to DNA and binding a short segment of RNA to DNA, which will be used to synthesize daughter strand; only polymerase known to be associated with a primase
19
Q
Pol ε
A
Synthesizes daughter strand of DNA using leading strand as a template
20
Q
Pol δ
A
Synthesizes daughter strand of DNA using lagging strand as a template; fills in gaps between Okazaki fragments
21
Q
PCNA
A
Proliferating cell nuclear antigen, clamps DNA polymerase onto DNA
22
Q
RCF
A
Replication factor C, loads PCNA clamp onto DNA
23
Q
RPA
A
Replication factor A, binds and stabilizes ssDNA during replication
24
Q
DNA ligase
A
Covalently links Okazaki fragments after they are synthesized
25
DNA Polymerase γ
Synthesizes mtDNA
26
DNA Polymerase β
Involved in base excision repair
27
Catalytic triad
Catalytic machinery of serine proteases - charge-relay comprising side-chain functional groups of aspartic acid, histidine, and serine
Interact to enable alcohol group on serine to make it behave like an alkoxide
Makes serine a good nucleophile and stabilizes transition state
28
Steps of serine protease catalysis
1. Binding of substrate
2. Attack by serine
3. Transition state
4. Release of products
29
Gibbs free energy
Predicts spontaneity of a reaction - when ∆G <0, spontaneous; ∆G=0 at eqm
∆G = RT ln Q
∆Gº = ∆G + RT ln Keq
30
Acyclovir & zidovudine
Nucleotide analogues that lack 3' OH for initiating nucleophilic attack, terminating chain elongation
31
Cdk
Cycling dependent kinase, regulate cell cycle by ensuring cellular checkpoints have been met
32
Li-Fraumeni syndrome
Inherited mutation of p53 (rather than spontaneous mutation) in the germ line tissue that predisposes affected individuals to develop cancer
33
Mut S
Enzyme that recognizes mismatches in DNA sequence
34
Mut L
Cofactor for Mut S
35
Mut H
Recognizes parental strand and cuts daughter strand containing mismatch, then resynthesizes DNA
36
RNA Polymerases I, II, and III
Pol I: makes rRNA
Pol II: binds to TATA box, synthesizes pre-mRNA
Pol III: synthesizes 5s rRNA
37
Steps of 5S rRNA synthesis
Bind TFIIIA and TFIIIC to promoter region in gene
Binding recruits TFIIIB
Pol III binds and RNA transcribed
38
Promoter
Region of DNA where TFs and RNA Pol bind, and where transcription is initiated
Function within a short distance (100-200bp) upstream of transcription initiation site
Position and orientation dependent
39
Enhancer
Short (50-1500bp) region of DNA where TFs bind, which can be located up to 1Mbp away from the gene it acts upon
Functional regardless of orientation
40
SWI/SNF
Nucleosome remodeling complex
41
Collagen types
Type I - Bone, skin, tendon
Type II - Cartilage
Type III - Reticulin (supporting mesh in soft tissues & skin)
Type IV - basement membrane
42
Steps of collagen synthesis
1. Chain synthesis inside cell as preprocollagen
2. Hydroxylation of lysine/proline residues
3. Glycosylation of hydroxylysine residues
4. Disulfide bond formation
5. Triple-helix formation
6. Secretion into the ECM
7. Hydrolysis of propeptides
8. Assembly into fibril
9. Assembly into fiber and formation of cross-links
43
Enzymes of collagen synthesis
Lysyl hydroxylase/prolyl hydroxylase - hydroxylate lysine/proline residues after chain synthesis
Lysyl oxidase - oxidize N-terminal of lysine side chain to make allysine, thus allowing adjacent lysine to form covalent bonds between collagen fibrils
44
Osteogenesis imperfecta
Glycine to cysteine substitution in triple-helix region of collagen I, which prevents monomers of the triple helix from coming together
Results in brittle bones, that break in utero or shortly after birth
45
Eherls-Danlos syndrome
Disease characterized by hyperflexibility of joints and skin hyper-extensibility
Caused by either improper processing of collagen (due to lack of enzyme) or defects in collagen genes (autosomal dominant)
46
Prion diseases
```
Kuru, Creudzfeldt-Jacob disease - caused by misfolded prion protein
Misfolded form (beta-sheets, insoluble) induces conformational change in normal form (alpha-helical)
```
47
Classes of enzymes:
1) Oxidoreductases
2) Transferases
3) Hydrolases
4) Lyases
5) Isomerases
6) Ligases
1) Oxidation-reduction
2) Transfer of a chemical group
3) Lysis by water
4) Cleavage not using water
5) Change of molecular configuration
6) Joining two compounds
48
Properties of serine proteases
Enzymes that have a catalytic triad consisting of aspartic acid, histidine, and serine (at positions 102, 57, and 195).
Substrate binds, is attacked by ser-OH; transition state is stabilized, and products are released
Examples: trypsin, chymotrypsin, elastase
49
Essential features of substrate binding to enzymes
1) Active site usually in a crevice that is a small part of the enzyme
2) Substrate is bound by multiple weak interactions
3) Binding is specific
4) Substrate placed in correct orientation for manipulation
50
Michaelis-Menten kinetics
At low [S], velocity of the rxn is roughly proportional to [S].
With increasing [S], velocity changes until enzyme is saturated at v = Vmax
Equation: v = Vmax * ([S]/(Km + [S]))
Km = [S] at 1/2 Vmax
51
Lineweaver-Burk plots
Plot inverse of MM equation in order to more precisely determine Vmax
Equation: 1/v = (Km/Vmax)(1/[S]) + 1/Vmax
y-intercept: 1/Vmax
x-intercept: -1/Km
52
Gibbs free energy
Predicts spontaneity of chemical reactions
∆Gº = -RT ln K
∆G = ∆Gº + RT ln Q = RT ln (Q/K)
If ∆G0 nonspontaneous; ∆G=0 equilibrium
When Q>K, ∆G>0 and rxn is nonspontaneous
53
Correlation between Km and affinity of enzyme for substrate
Km loosely corresponds to the inverse of affinity of enzyme for substrate
If Km is small --> affinity is high
If Km is large --> affinity is low
54
Zymogen
Inactive enzyme precursor, undergoes proteolytic cleavage for activation
55
Thrombin: precursor, converting complex, localization
Precursor: Prothrombin
Converting complex: Factor V, Factor X, Ca2+, phospholipids
Localization: Prothrombin - membrane-bound (due to gamma-carboxylation of glutamate residues and calcium binding), cleaved and released
56
Gamma carboxylation of prothrombin
Process that enables calcium binding and thus anchoring of prothromin to cell membrane
Requires vitamin K
57
Warfarin
Vitamin K analog, inhibits gamma-carboxylation and thus reduces the amount of thrombin that can be made
58
α1-antitrypsin
Elastase inhibitor secreted by liver which is necessary for protection of lung tissue
Cigarette smoke oxidizes methionine residue critical for function, resulting in increased elastase activity and emphysema
59
Amino acids commonly phosphorylated
Serine, threonine, tyrosine
| Phosphorylation changes the charge of the enzyme, changing its function
60
Competitive inhibitor
Reversible inhibitor of enzymes, binds to active site but cannot be acted upon by the enzyme
Do not alter Vmax - change apparent Km
61
Noncompetitive inhibitor
Allosteric inhibitors of enzymes; do not resemble substrate
| Reduce Vmax -- effectively reduce the amount of enzyme present
62
DIFP
Diiospropylfluorophosphate - irreversible inhibitor of serine proteases, especially acetylcholine esterase
63
Rb (gene and protein)
Tumor suppressor gene, protein binds E2F which regulates DNA transcription and cell cycle progression; when mutated E2F no longer bound and abnormal cell growth occurs
64
p53
Tumor suppressor that is mutated in ~50% of all cancers; acts on p21 gene which halts cell cycle. When mutated, cells replicate damaged DNA
65
Oncogene
Mutated copy of a cellular gene that has the potential to cause cancer
66
3 subclasses of signal transduction receptors
1) Membrane penetrating enzymes
2) Nuclear-localizing receptors
3) G-protein coupled receptors (7 membrane spanning domain proteins)
67
What enzyme catalyzes the hydrolysis of peptides on the C-terminal side of phenylalanine, tyrosine and tryptophan?
Chymotrypsin.
68
What amino acids make up the catalytic triad in a serine protease?
Aspartate, histidine and serine.
69
Do enzymes change their structure after catalysis?
No. At the end of the reaction cycle they are the same as when they started.
70
When the Gibbs free energy (G) of a reaction is negative, that reaction is ______.
Spontaneous.
71
When the Gibbs free energy (G) of a reaction is positive, that reaction is ______.
Non-spontaneous.
72
When the Gibbs free energy (G) of a reaction is zero, that reaction is ______.
At equilibrium.
73
True or False. All exothermic reactions are spontaneous.
False. Delta G can be negative (indicating a spontaneous reaction) even when delta H is positive. This occurs when delta S (the change in entropy) is positive.
74
True or False. Reactions in the body are in equilibrium.
False.
75
How do enzymes affect the energy of reactions?
Enzymes lower the activation energy. They accelerate the rate of reactions, but do not change the potential energy of the substrates or products.
76
How does the activation energy affect the speed of a reaction?
In general, the larger the activation energy the slower the reaction.
77
Define catabolism.
Burning fuel to make ATP.
78
Define anabolism.
Burning energy (usually ATP) for biosynthetic processes, active transport and/or mechanical work.
79
How can one determine reaction velocity?
By measuring the amount of product formed per unit time.
80
What kinetic parameters can be extracted from a Michaelis-Menten kinetics graph?
Vmax, the maximum velocity of the catalyzed reaction, and Km, the substrate concentration required to achieve half the maximum velocity.
81
When is Km equal to the substrate concentration in a Michaelis-Menten Kinetics graph?
When the substrate concentration is at half of Vmax.
82
Delta G for ATP hydrolysis (ATP + H2O -> ADP + Pi) is -7.3 kcal/mole. How much energy is required to perform the reverse reaction?
+7.3 kcal/mole.
83
What is a cofactor?
Cofactors are typically small molecules that help promote catalysis. Many vitamins act as cofactors.
84
Which enzyme is deficient in individuals with methylmalonic acidemia?
Methylmalonyl mutase.
85
What is the cofactor for methylmalonyl mutase?
Vitamin B12.
86
What are the substrates and products of methylmalonyl mutase?
The enzyme converts methylmalonyl CoA to succinyl CoA.
87
True or False. Generally, the atoms in an enzyme that bind to a substrate are different than the atoms that participate in the catalysis of a reaction.
True.
88
What are the four steps, in order, of a reaction catalyzed by serine proteases?
1. Binding of substrate, 2. attack by serine, 3. stabilization of transition state, and 4. release of products.
89
What is an oxyanion hole and what is its function?
It is a structural pocket in an enzyme that stabilizes an oxyanion (i.e. stabilizes the transition state).
90
The initial enzyme velocity proportional to what?
The amount of substrate.
91
The y-intercept in Lineweaver-Burk plots corresponds to what kinetic parameter?
+ 1/Vmax.
92
The x-intercept in Lineweaver-Burk plots corresponds to what kinetic parameter?
- 1/Km.
93
The slope in Lineweaver-Burk plots corresponds to what kinetic parameter?
Km/Vmax.
94
What can elevated enzyme activity in blood plasma indicate?
Tissue damage.
95
What is a zymogen?
An inactive enzyme precursor.
96
How are zymogens activated?
By proteolytic cleavage.
97
What is the prothrombin-converting complex and what are its components?
The prothrombin-converting complex cleaves prothrombin into its active form, thrombin. It contains calcium, phospholipids, and two coagulation proteins, Factor V and Factor X.
98
What do Factor V and Factor X do to thrombin?
Factor V cleaves prothrombin to prethrombin. Factor X cleaves prethrombin to thrombin.
99
What happens to the prethrombin segment between residues 15 and 20 after prethrombin is cleaved to thrombin?
In the active enzyme, residue 16 repositions itself. This results in the proper formation of the catalytic triad, which contains the active nucleophile residue, serine 195.
100
Where in the cell is the mature form of thrombin generated?
On the cell membrane surface.
101
What class of enzymes is involved in activating prothrombin and fibrinogen in the blood clotting cascade?
Serine proteases.
102
Prothrombin is modified by gamma-carboxylation of which amino acid residues at its N-terminus?
Glutamate.
103
Why is it important for prothrombin to be gamma-carboxylated?
It allows for calcium binding, which is required to anchor prothrombin to the cell membrane.
104
Which enzyme catalyzes the conversion of soluble fibrinogen to insoluble fibrin?
Thrombin.
105
Does gamma-carboxylation of thrombin regulate enzyme activity?
No. Although gamma-carboxylation is required for formation of the active enzyme for blood coagulation, it does not directly regulate enzyme activity.
106
Which cofactor is required for gamma-carboxylation of prothrombin?
Vitamin K.
107
Name a vitamin K analogue that is used to treat thrombosis (blood clots).
Warfarin.
108
Warfarin is a common anti-coagulant. How does it work?
It inhibits the gamma-carboxylation reaction of prothrombin, thereby reducing the number of prothrombin molecules on the cell surface. This reduces the amount of active thrombin that can be synthesized by a cell.
109
Heparin is a common anti-coagulant. How does it work?
It promotes the binding of antithrombin to thrombin, thereby reducing blood clotting.
110
How is thrombin inactivated?
Thrombin is inactivated when a protein named antithrombin binds to its active site.
111
What is the role of alpha1-antitrypsin in the lungs?
It inhibits neutrophil-produced elastase in the lungs.
112
What is the clinical consequence of alpha1-antitrypsin deficiency with regards to the lungs?
Alpha1-antitrypsin deficiency may lead to lung destruction and emphysema.
113
How does cigarette smoking affect the activity of alpha1-antitrypsin?
Cigarette smoke oxidizes a methionine residue on alpha1-antitrypsin that is involved in binding elastase. Oxidation of this residue prevents inhibition of elastase. (Recall that elastin is the cross-linked protein that makes lung tissue spongy).
114
Which amino acids can typically be modified by enzymatic phosphorylation/dephosphorylation?
Serine, threonine and tyrosine.
115
How do competitive inhibitors block enzymatic activity?
They reversibly compete with the enzyme substrate for the active site. They usually resemble the substrate in structure, so they are able to fit into the active site but cannot be acted upon by the enzyme.
116
Define Ki.
Ki measures the affinity of an enzyme for a certain inhibitor. The smaller the Ki, the greater the effectiveness of the inhibitor.
117
Define Km.
Km measures the affinity of an enzyme for its substrate. The smaller the Km, the greater the enzyme's affinity for its substrate. Km is also defined as 1/2 Vmax.
118
What is the effect of competitive inhibitors on Km and Vmax?
Competitive inhibitors increase Km but do not alter Vmax.
119
What is the effect of noncompetitive inhibitors on Km and Vmax?
Noncompetitive inhibitors lower Vmax but do not alter Km.
120
How do noncompetitive inhibitors block enzymatic activity?
Noncompetitive inhibitors block product formation by binding to a site other than the active site. They are able to bind the enzyme irrespective of whether or not a substrate is present.
121
What are enzyme activators?
They are positive effectors that promote the enzyme to exist in its active form, where it is a more effective catalyst.
122
True or False. Allosteric enzymes often catalyze the first step of a reaction sequence.
True.
123
What is meant by the term 'feedback inhibition'?
Feedback inhibition is a phenomenon by which the end product of a reaction or sequence of reactions inhibits the enzyme or enzymatic cascade. When sufficient product is produced, the system automatically turns itself off.
124
List three common characteristics of committed steps.
1. They are functionally irreversible 2. They occur early in the enzymatic pathway 3. They occur in only one pathway
125
Name an inhibitor of the enzyme aspartate transcarbamoylase (ATCase).
Cytidine triphosphate (CTP).
126
Name an activator of the enzyme aspartate transcarbamoylase (ATCase).
Adenosine triphosphate (ATP).
127
What is the difference between carcinomas, sarcomas, leukemias and lymphomas?
Carcinomas arise from epithelial cells. Sarcomas: connective tissues, muscle, cartilage, fat, or bone. Leukemias and lymphomas: blood cells.
128
What are tumor suppressor genes? List some examples of proteins encoded by these genes.
They are genes that encode proteins that help control cell growth and proliferation. Generally, the proteins encoded by tumor suppressor genes exert a repressive effect on the cell cycle. (Well known examples include p53, pRb, WT1, BRCA1, BRCA2, NF1, APC and PTEN.)
129
True or False. Having one functional allele of Rb is protective against cancer.
True. Loss of both alleles is necessary for tumor formation. This is true of most tumor suppressors, although p53 is a notable exception.
130
True or False. The retinoblastoma gene is a proto-oncogene.
False. RB is a tumor suppressor gene.
131
Which cyclins are involved in inactivating pRB?
Cyclins D and E.
132
Which transcription factor is inactive when bound to pRB?
E2F.
133
When pRB is phosphorylated by cyclin-dependent kinases, it releases the molecule E2F. What is the role of E2F in the nucleus?
It stimulates the synthesis of proteins required for the S-phase of the cell cycle such as the polymerase-alpha/primase complex.
134
What condition is caused by germline mutations of the gene that encodes p53?
Li-Fraumeni syndrome.
135
What is the outcome with regards to cell survival when p53 detects DNA damage in the cell?
There are two possible outcomes: p53 may either arrest the cell at the G1/S checkpoint so that DNA can be repaired, or if the damage is too extensive, p53 may induce apoptosis.
136
Which gene is a target of p53 when it comes to halting the cell cycle?
The gene for p21, which codes for a protein that is able to halt the cell cycle in the G1 phase.
137
How does p21 halt the cell cycle?
It binds to and inhibits the cyclin-CDK2 complex. Since CDK2 activity is required for the cell to advance through the G1/S checkpoint, inhibiting cyclin-CDK2 will halt the cell in the G1 phase.
138
True or False. The p53 gene is tumor suppressor gene.
True.
139
What are proto-oncogenes?
They are genes that encode growth-promoting proteins.
140
What are oncogenes?
They are mutated copies of proto-oncogenes.
141
How many alleles of a proto-oncogene must be mutated before tumor formation can occur?
One.
142
What family of receptors binds to PDGF and insulin?
Tyrosine kinase receptors.
143
Where are tyrosine kinase receptors located in the cell?
The cell membrane.
144
What oncogene encodes part of the PDGF receptor?
The sis oncogene.
145
Where are steroid receptors located in the cell?
They can be found in the cytoplasm or nucleus.
146
What family of receptors binds to glucagon?
The seven trans-membrane spanning receptors. This large class of receptors are also known as 7TM receptors and GPCRs (G-protein coupled receptors).
147
What does the erb-B oncogene encode?
It encodes a modified form of the EGF receptor. The result is that the receptor will always produce intracellular signals, even in the absence of EGF.
148
When bound to GTP, RAS is in its ____________ (active/inactive) form.
Active.
149
How does a mutation of the ras gene affect the signaling activity of its protein product, RAS?
Mutations that occur in the GTPase domain of RAS will reduce the protein's ability to hydrolyze GTP. This will result in excessive signal transduction to the nucleus. 25% of cancers involve Ras mutants.
150
True or False. The neurofibromatosis type 1 (NF1) gene is a tumor suppressor gene.
True. The gene contains a GAP (GTPase activating domain).
151
How does a mutation in the NF1 gene affect the signaling of its protein product, neurofibromin?
NF1 deletion mutations lead to loss neurofibromin GAP domain (GTPase activating domain) activity. As a result, neurofibromin will not be able to activate the GTPase on RAS, so RAS will be "stuck" in its on position, sending excess signals to the nucleus.
152
What is the most common way in which a cell can regulate the activity of its transcription factors?
Reversible phosphorylation.
153
Which transcription factors form a complex on AP1 sites on DNA?
Fos and Jun. The complex of Fos and Jun is known as AP1.
154
How does a mutation in the AP1 gene affect cell growth?
Normally, the expression of Fos and Jun increases only transiently. A mutation that will affect the transient nature of Fos and Jun expression may lead to constitutive expression of these proteins. As a result, cell growth will be continuous instead of transient.
155
Overexpression of which transcription factor is associated with increased risk of developing Burkitt's lymphoma?
MYC.
156
What is the role of the transcription factor MYC?
It binds to enhancer sequences and recruits histone acetyltransferases, thereby regulating the expression of many genes. It helps to force cells forward through the cell cycle.
157
What is the nature and location of the mutation associated with Burkitt's lymphoma?
The mutation is a reciprocal translocation between the c-myc gene and the immunoglobin heavy chain genes (IgH).
158
Simian virus 40 (SV40) T-antigen binds which tumor suppressor proteins?
p53 and pRb.
159
The E6 gene of human papillomaviruses binds to which human tumor suppressor gene product?
p53.
160
The E7 gene of human papillomaviruses binds to which human tumor suppressor gene product?
pRB.
161
How do the viral proteins of human papillomaviruses affect human pRB?
The viral E7 protein binds to pRB to induce the release of the E2F transcription factor, allowing E2F to bind promoters and activate the transcription of genes in an unregulated manner.
162
How do the viral proteins of human papillomaviruses affect human p53?
The viral E6 protein is able to bind to human p53 and induce the proteolysis of p53 via the ubiquitin pathway. This allows the cell to not only go through the cell cycle without checking for DNA damage, but also to evade apoptosis.
163
Which viral encoded protein in the human papillomaviruses genome is most important for viral genome replication?
E1.
164
Which viral encoded protein in the human papillomaviruses genome is required for viral genome transcription?
E2.
165
What are the six pathologic characteristics of tumor cells?
1. Self sufficiency through growth signals (for example, activation of RAS) 2. Insensitivity to anti-growth signals (for example, loss of pRB) 3. Evasion of apoptosis 4. Limitless replicative potential (for example, activation of telomerase) 5. Sustained angiogenesis 6. Metastasis.
166
Adenomatous polyposis of the colon is associated with a mutation of which tumor suppressor gene?
APC.
167
What is cancer metastasis?
The spread of cancer from one part of the body to another.
168
Which carbon of monosaccharides is chemically reactive?
The anomeric carbon.
169
What is a glycoside?
The product of the condensation of a sugar with a hydroxyl-containing molecule.
170
What is the difference between a glucoside and a galactoside?
Glucosides are glycosides that have a glucose, whereas galactosides have a galactose.
171
What is a glycosidic bond?
A covalent bond that joins a sugar to the hydroxyl group of another molecule.
172
Maltose is composed of which sugars bound in what linkage?
Two molecules of glucose in an alpha(1->4)-linkage.
173
Lactose is composed of which sugars bound in what linkage?
Galactose and glucose in a beta(1->4)-linkage.
174
Sucrose is composed of which sugars bound in what linkage?
Glucose and fructose in an alpha(1->2)-linkage.
175
What is the composition and structure of amylose?
Amylose is a starch composed of glucose molecules in alpha(1->4)-linkages. Its structure is that of an unbranched polymer that typically forms a helical coil within cells.
176
What is the composition and structure of amylopectin?
Amylopectin is a starch composed of glucose polymers arranged in alpha(1->4)-linkages. It has branches in alpha(1->6)-linkages every 10-12 residues.
177
What is the composition and structure of glycogen?
Glycogen is a carbohydrate composed of glucose polymers arranged in alpha(1->4)-linkages. It has branches in alpha(1->6)-linkages every 8-10 residues and it exists as spherical particles in cells.
178
What is the composition and structure of cellulose?
Cellulose is composed of glucose polymers arranged in beta(1->4)-linkages. It is typically unbranched.
179
What is the composition and structure of dextrans?
Dextrans are composed of glucose polymers arranged in alpha(1->6)-linkages. They have some branches in alpha(1->3)-linkages.
180
What are glycosaminoglycans (GAGs)?
They are long unbranched polysaccharides of repeating anionic disaccharides. They may be sulfated and are an important component of connective tissues.
181
What is a proteoglycan?
Glycosaminoglycans that are covalently linked to a protein.
182
Which glycosaminoglycan (GAG) is not linked to a core protein?
Hyaluronic acid.
183
Alpha(1->4)- vs. beta(1->4)-linkages. Which can we NOT digest?
Beta(1->4)-linkages.
184
What is the composition and location of hyaluronic acid?
Hyaluronic acid is composed of repeating disaccharides of D-glucuronic acid and N-acetylglucosamine. It is typically found in connective tissue like synovial fluid in joint spaces and in the vitreous fluid of the eye.
185
Which chemical reaction involves the formation of a Schiff base between the aldehyde of a sugar and the amino group of a protein to generate a ketoamine?
Glycation.
186
True or False. Glycation is a form of tissue damage.
True.
187
What is the clinical significance of hemoglobin A1c (HbA1c)?
HbA1c provides a 3-month 'history' of blood glucose levels.
188
What is aggrecan?
It is a proteoglycan (composed of chondrotoin sulfate attached to collagen type II) that acts as a shock absorber by cycling water in and out of cartilage.
189
Which nucleotide is NOT involved in the activation of sugars?
Adenine.
190
Which amino acids are involved in N-linked glycosylation?
Asparagine (almost always).
191
Which amino acids are involved in O-linked glycosylation?
Serine and threonine.
192
What is glycosylation?
An enzymatic reaction for secreted or extracellular protein (including proteins that are meant to be stored in the ER lumen).
193
Which glycoprotein is typically NOT secreted from cells?
O-linked N-acetylglucosamine (O-GlcNac).
194
In which cellular compartment are O-linked glycoproteins usually glycosylated?
The Golgi apparatus.
195
Which class of enzymes adds sugars to a growing O-linked glycoprotein?
Glycosyltransferases.
196
True or False. O-links of glycoproteins have carbohydrate molecules first added as a pre-assembled 14 sugar block.
False. The statement is true for N-linked glycoproteins.
197
What lipid carrier molecule is used for the synthesis of the branched oligosaccharide of N-linked glycoproteins?
Dolichol phosphate.
198
Which sugars are used for the synthesis of the initial branched chain oligosaccharide of N-linked glycoproteins?
N-acetylglucosamine, mannose and glucose.
199
Where in the cell are sugars added to proteins to form N-linked glycoproteins?
The ER membrane.
200
Which antibiotic inhibits the addition of N-acetylglucosamine-phosphate to dolichol phosphate?
Tunicamycin.
201
What class of enzymes is responsible for degradation of glycoproteins?
Glycosidases.
202
Deficiency of acid glucosidase results in what storage disease?
Pompe's syndrome.
203
What is the enzymatic defect in Hunter syndrome?
Iduronate sulfatase.
204
What are proteoglycans?
Macromolecules consisting of polysaccharide glycosaminoglycan chains that are attached to core proteins.
205
What is the most abundant glycosaminoglycan in the human body?
Condrotoin sulfate.
206
Where is keratan sulfate type I typically found in the human body?
The cornea.
207
Where is keratan sulfate type II typically found in the human body?
Cartilage.
208
Which class of proteins bind carbohydrates?
Lectins.
209
What is the difference between the terminal sites of Type A, B and O blood groups?
Type A blood has UDP-N-acetylgalactosamine as a terminal residue, Type B has UDP-galactose and Type O has neither.
210
H-pylori preferentially binds to gastric epithelial cells of individuals with which blood type?
O-type.
211
What is the net chemical equation for the reactions of anaerobic glycolysis?
Glucose + 2 ADP + 2 Pi -> 2 Lactate + 2ATP + 2 H2O.
212
Which cell type in the human body relies only on glycolysis as a source of ATP?
Erythrocytes (red blood cells) only.
213
What is the major source of ATP in skeletal muscle at rest? During exercise?
Oxidative metabolism at rest; both oxidative phosphorylation and glycolysis during exercise.
214
Which enzyme is most frequently deficient in hemolytic anemias?
Pyruvate kinase.
215
In which cellular compartment does glycolysis occur?
The cytoplasm.
216
Which enzyme(s) converts glucose to glucose-6-phosphate?
Hexokinase and glucokinase.
217
What is the reaction catalyzed by phosphohexose isomerase?
Glucose-6-phosphate -> fructose-6-phosphate.
218
Which glycolytic enzymes catalyze irreversible reactions?
Hexokinase, phosphofructokinase-1(PFK-1) and pyruvate kinase.
219
Which glycolytic enzymes use ATP to phosphorylate their substrate, thereby producing ADP?
Hexokinase and phosphofructokinase-1 (PFK-1).
220
Which glycolytic enzymes catalyze reactions that yield ATP?
Phosphoglycerate kinase and pyruvate kinase.
221
Which glycolytic enzymes catalyze reactions that yield NADH?
Glyceraldehyde-3-phosphate dehydrogenase.
222
Which glycolytic enzymes use inorganic phosphate, and not ATP, to phosphorylate their substrates?
Glyceraldehyde-3-phosphate dehydrogenase (very important!).
223
What is the committed step in glycolysis?
The phosphofructokinase-1 reaction (PFK1).
224
What reaction does phosphofructokinase-2 (PFK-2) catalyze?
Fructose-6-phosphate + ATP -> fructose-2,6-bisphosphate + ADP.
225
In glycolysis, what reaction does the enzyme aldolase catalyze?
Fructose-1,6-bisphosphate -> glyceraldehyde-3-phosphate + dihydroxyacetone-phosphate.
226
The aldolase reaction in glycolysis yields two products. Which one of these products is a direct glycolytic intermediate?
Glyceraldehyde-3-phosphate is the substrate for the next steps of glycolysis. Dihydroxyacetone-phosphate must be isomerized into glyceraldehyde-3-phosphate in order to continue through glycolysis.
227
Which enzyme can be inhibited by the molecule 2-deoxyglucose?
Hexokinase.
228
Which molecules are able to inhibit phosphofructokinase-1 (PFK-1)?
ATP, citrate and fatty acids.
229
Which molecules are able to activate, or relieve inhibition of, phosphofructokinase-1 (PFK-1)?
ADP, AMP, and fructose-2,6-bisphosphate.
230
Which glycolytic enzyme exhibits negative cooperativity?
Glyceraldehyde-3-phosphate dehydrogenase.
231
Which enzyme reversibly isomerizes dihydroxyacetone-phosphate to glyceraldehyde-3-phosphate?
Triose phosphate isomerase.
232
From which vitamin is NAD+ derived?
Vitamin B3 (niacin).
233
How many molecules of NAD+ can the enzyme glyceraldehyde-3-phosphate dehydrogenase bind?
4
234
What is substrate-level phosphorylation?
Substrate-level phosphorylation refers to the formation of ATP (or GTP) by the direct transfer of a phosphate group from a reactive metabolic intermediate to ADP (or GDP).
235
What kind of a reaction is catalyzed by the enzyme enolase?
Dehydration/hydration.
236
The enzyme enolase is strongly inhibited by which molecule?
Fluoride.
237
Which enzyme catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate (PEP)?
Enolase.
238
Which enzyme catalyzes the conversion of phosphoenolpyruvate (PEP) to pyruvate and ATP?
Pyruvate kinase.
239
How many moles of ATP does pyruvate kinase generate per glucose molecule?
2
240
Which molecules stimulate the activity of pyruvate kinase?
Fructose-1,6-bisphosphate. This phenomenon is called feed-forward stimulation.
241
Which molecules are able to inhibit pyruvate kinase?
Alanine, NADH, ATP, fatty acids, and succinyl-CoA.
242
What is the role of the enzyme lactate dehydrogenase under anaerobic conditions?
Lactate dehydrogenase transfers electrons from NADH to pyruvate, reducing pyruvate to lactate to regenerate NAD+. Regeneration of NAD+ is required if the cell is to continue with glycolysis under anaerobic conditions (remember that NAD+ is a required cofactor for glyceraldehyde-3-phosphate dehydrogenase).
243
Most of the NAD+ in cells is synthesized from niacin (vitamin B3). However, a small amount of NAD+ may be synthesized from which amino acid?
Tryptophan.
244
Niacin deficiency may result in which condition?
Pellagra.
245
List the main symptoms of pellagra.
The symptoms of pellagra are sometimes referred to as 'the four D's': diarrhea, dementia, dermatitis and death.
246
In which cell compartment do the reversible interconversions of lactate, alanine and pyruvate occur?
Cytoplasm.
247
In which cell compartment do the irreversible conversions of pyruvate to oxaloacetate and acetyl-CoA occur?
Mitochondria.
248
Which glycolytic enzymes are allosterically regulated?
Hexokinase, phosphofructokinase-1 (PFK-1) and pyruvate kinase.
249
Which glycolytic enzymes are regulated by phosphorylation?
Pyruvate kinase is inactivated by phosphorylation.
250
The hormone insulin induces the synthesis of which glycolytic enzymes?
Glucokinase and pyruvate kinase.
251
What is the net yield of ATP in the conversion of one glucose molecule to two pyruvates during glycolysis?
Two moles of net ATP are produced per one mole of glucose.
252
Which glycolytic intermediate(s) can be used to synthesize glycogen, polysaccharides, glycoproteins and pentoses?
Glucose-6-phosphate.
253
The pentose phosphate shunt produces NADPH and pentose sugars. Pentose sugars from this shunt may enter the glycolytic pathway as which glycolytic intermediate(s)?
Fructose-6-phosphate and glyceraldehyde-3-phosphate.
254
Which glycolytic product(s) can be reduced to glycerol-3-phosphate, a precursor for fatty acid and phospholipid biosynthesis?
Dihydroxyacetone-phosphate.
255
Which amino acid(s) can be inter-converted with 3-phosphoglycerate?
Serine.
256
Pyruvate can be inter-converted with which amino acid(s)?
Alanine.
257
Which glycolytic intermediate(s) can be oxidized to acetyl-CoA, which is used for synthesis of fatty acids, cholesterol, steroid hormones and oxidative metabolism?
Pyruvate.
258
Which toxic substance is able to inhibit hexokinase?
2-deoxyglucose.
259
Which step of glycolysis is affected by pentavalent arsenic?
Pentavalent arsenic prevents the production of ATP by glyceraldehyde-3-phosphate dehydrogenase. Note, however, that it does not stop the process of glycolysis. It only prevents the net gain of ATP.
260
Which toxic substances can react with the sulfhydryl group of glyceraldehyde-3-phosphate dehydrogenase and block the glycolytic process altogether?
Mercury compounds.
261
How does the regulation of lactate dehydrogenase in skeletal muscle differ from that in cardiac muscle?
In skeletal muscle, when more pyruvate is produced than can enter the TCA cycle, pyruvate will be converted to lactate by lactate dehydrogenase. In the heart, however, rising pyruvate concentrations will inhibit lactate dehydrogenase. This is because lactate is an acid that, in excess, can cause muscle cramps. Therefore, pyruvate inhibition of lactate dehydrogenase in the heart has a protective effect on cardiac function.
262
What reaction does the enzyme fructokinase catalyze?
Fructose + ATP -> fructose-1-phosphate + ADP.
263
What are the substrates for the enzyme aldolase B?
Aldolase B can cleave both fructose-1-phosphate and fructose-1,6-bisphosphate.
264
The enzyme aldolase B cleaves fructose-1-phosphate into which two products?
Dihydroxyacetone-phosphate, which can enter glycolysis, and glyceraldehyde, which must be phosphorylated before it can enter glycolysis.
265
Deficiency of which enzyme results in dietary fructose intolerance that is accompanied by accumulation of fructose-1-phosphate?
Aldolase B.
266
Deficiency of fructokinase results in which condition?
Hereditary fructosuria.
267
How does aldolase B deficiency affect the blood concentration of glucose, free phosphorous and uric acid?
The concentration of glucose falls because fructose-1-phosphate inhibits glycogen breakdown. The concentration of free phosphorous falls because the cellular supply of phosphorous becomes trapped in fructose-1-phosphate. The concentration of uric acid rises because of an increase in the metabolism of purine nucleotides.
268
Which enzyme catalyzes the phosphorylation of mannose to mannose-6-phosphate?
Hexokinase.
269
How does mannose enter the glycolytic pathway?
Mannose is phosphorylated to mannose-6-phosphate by hexokinase. Mannose-6-phosphate is then isomerized to fructose-6-phosphate by phosphomannose isomerase.
270
What is the main source of dietary galactose?
Lactose (found in dairy products).
271
Which enzyme catalyzes the phosphorylation of galactose to galactose-1-phosphate?
Galactokinase.
272
Which enzyme catalyzes the reversible isomerization of glucose-6-phosphate to glucose-1-phosphate?
Phosphoglucomutase.
273
Galactose-1-phosphate is toxic to cells when present in excess. Which enzyme prevents the accumulation of galactose-1-phosphate by catalyzing its conversion to UDP-galactose?
Galactose-1-phosphate uridyltransferase.
274
What coenzyme is required for the interconversion of UDP-galactose with UDP-glucose by the enzyme UDP-galactose-4-epimerase?
NAD+.
275
Which enzyme permits the glycosylation of proteins and lipids with galactose even in the absence of dietary galactose?
UDP-galactose-4-epimerase. This enzyme can isomerize UDP-glucose to UDP-galactose, and can therefore produce UDP-galactose even when galactose is absent in the diet.
276
Name three enzymes of galactose metabolism that, when deficient, can lead to galactosemia (accumulation of galactose in the blood).
Galactokinase, galactose-1-phosphate uridyltransferase, and UDP-galactose-4-epimerase.
277
Accumulation of which metabolite in the lens of the eye can lead to the development of cataracts in individuals with galactokinase deficiency?
Galactitol.
278
Lack of growth in newborns, accumulation of galactose-1-phosphate and accumulation of galactitol-1-phosphate are all associated with the deficiency of what enzyme?
Galactose-1-phosphate uridyltransferase.
279
Which organ metabolizes the majority of the alcohol absorbed into the bloodstream following ingestion?
The liver.
280
Name the primary enzyme that catalyzes the conversion of alcohol into acetaldehyde.
Alcohol dehydrogenase (ADH).
281
What is the microsomal ethanol oxidizing system (MEOS) and in which cellular compartment is it found?
MEOS is found in the smooth endoplasmic reticulum. Its activity increases during chronic alcohol consumption, thereby accounting for increased alcohol tolerance in heavy drinkers.
282
The build up of which alcohol metabolite makes people ill when consuming too much alcohol?
Acetaldehyde.
283
What is the chemical equation for the reaction catalyzed by aldehyde dehydrogenase?
Acetaldehyde + NAD+ -> acetate + NADH + H+.
284
What are two ways in which alcohol consumption can lead to acidosis?
1. Acetate, an alcohol metabolite, may appear in the blood and lead to acidosis 2. Metabolism of alcohol depletes cellular stores of NAD+. To restore NAD+, there will be an increased conversion of pyruvate to lactate by lactate dehydrogenase, which can lead to lactic acidosis.
285
Wernicke-Korsakoff syndrome can arise from deficiency of which vitamin?
Vitamin B1 (thiamine).
286
Which enzyme catalyzes the phosphorylation of fructose to fructose-6-phosphate?
Hexokinase.
287
What is the reaction catalyzed by fructokinase?
Fructose -> fructose-1-phosphate.
288
What is the reaction catalyzed by galactokinase?
Galactose -> galactose-1-phosphate.
