1. What’s the connection between UCP3 (Uncoupling protein 3) and MDMA?

UCP3 is a protein expressed in the skeletal muscle, which is responsible for thermogenesis and
limiting production of three oxygen radicals. MDMA binds to UCP3 and leads to death through
hyperthermia and subsequent rhabdomyolysis.

2. Explain Warburg effect

Warburg effect highlights the tendency of cancer cells to produce energy through anaerobic
glycolysis in opposition to more effective oxidative phosphorylation pathway in healthy cells. It
results in rapid production of ATP and supports growth of cancer cells through other pathways,
however, it results in excessive production of hydrogen ions, low yield of ATP and causes cancer
patients to lose weight as their glucose is being excessively metabolized.

3. Give the mnemonic for substrates used to produce malate:

Michael Asked Anna Out:
Malate  Asparagine, Aspartate, Oxaloacetate

4. Explain why does the insufficient amount of oxygen leads to anaerobic glycolysis?
When no oxygen is present, NADH produced from oxidation of glucose to pyruvate cannot be
oxidized itself to NAD+ and used in conversion of pyruvate to acetyl-coA. Instead, the accumulated
NAD is used to reduce pyruvate to lactate and is converted to NADP+ BUT it can be only used to
convert glucose to pyruvate in other to sustain anaerobic glycolysis.

5. What are the possible routes of glucose transport?

 First route: through Na+/glucose symporter
 Glucose transporters: GLUT1 and GLUT3 in brain (high Km), GLUT2 in liver (high Km, insulin
b-cell dependent), GLUT 4 in muscles (insulin-dependent), GLUT5 in gut (fructose
metabolism)
5 guut candies and 13 brownies go 2 liver 4 muscles
6. List 4 steps of TCA cycle that can be inhibited (as well as their inhibitors)
All of the steps are inhibited by NADH and ATP, with some additional molecules:
1. Pyruvate to acetyl coA (by pyruvate dehydrogenase): inhibited by acetyl-coA
2. Acetyl coA to citrate (by citrate synthase): inhibited by succinyl coA and citrate
3. Isocitrate to a-ketoglutarate (by isocitrate dehydrogenase): can be also stimulated by
NAD+ and ADP
4. A-ketoglutarate to succinyl coA (by a-ketoglutarate dehydrogenase complex): inhibited by
succinyl coA
7. How TCA cycle is connected to electron transport chain?
Succinate dehydrogenase is used as Complex II in electron transport chain, which gives accepted
electrons to ubiquinone protein (after FAD is reduced and malate is converted to fumarate).
8. Which of the enzymes of the TCA cycle is the only one not located in matrix (and what
reactions does it catalyze?):
The enzyme succinate dehydrogenase is incorporated in mitochondrial membrane and it
catalyzes the following reaction: FAD + malate  FADH2 + fumarate
9. List the symptoms of PDCD:
 P - poor muscle tone and coordination
 D - dull (mental retardation and seizures)
  C – lactic aCidosis
 D – don’t breathe well (respiratory problems)
10. What can be observed in patients with PDCD:
The condition usually presents as a set of neurological problems, however, further examination
can actually show brain lesions and defective symmetry of left and right hemisphere.
11. Give the mnemonic for the substrates used to produce succinyl CoA:
VAL IS MEking (making) THREads that Succ(k)!
Valine, isoleucine, methionine and threonine  succinyl CoA
12. Describe how GLUT1 transports glucose to the other site of the membrane
Glucose binds  Induces a conformational change  Glucose released inside the cell  Another
conformational change restores the binding site
13. Give mnemonic for the substrates used to produce pyruvate
Cys SPAT (on) Gly
Cysteine Serine Pyruvate Alanine Threonine Glycine
14. What are the three control points of glycolysis?
 Conversion of glucose to glucose-6-phosphate by hexokinase, inhibited by glucose-6-
phosphate
 Conversion of fructose-6-phosphate to fructose-1,6-biphosphate by fructose
phosphokinase, inhibited by ATP and citrate
 Conversion of phosphoenolpyruvate to pyruvate by 1-pyruvate kinase, inhibited by ATP
15. Describe how pyruvate is transformed to Acetyl CoA:
 Pyruvate loses CO2 molecule, which is used to form HETTP from TTP
 HETTP molecule is used to convert lipoamide to its reduced form of acetyl lipoamide
 Acetyl lipoamide transfers acetyl group to CoA molecule to form acetyl CoA
16. What is the common structural units of cytochromes?
All cytochromes contain haem group, which includes Fe (II) ion that can take up and release
electrons.
17. How uncoupling proteins (thermogenins) work?
Uncoupling proteins disrupt oxidative phosphorylation by causing a leak of hydrogen ions back to
matrix (which would be normally used by ATP synthase)
18. Why protons in mitochondria will flow back from intermembrane space into matrix?
When protons are pumped out of mitochondrial matrix by using energy from electron transport
chain, they generate a substantial positive charge in the intermembrane space. Matrix, therefore,
creative a negatively charged electromagnetic field which attracts protons  they flow back 
they flow through ATP synthase to produce energy.
19. Describe the pathology of Hereditary Leiomyomatosis and Renal Cell cancer:
Deficiency in fumarate hydratase causes overexpression of hypoxia inducing factors which then
lead to pseudohypoxia  cells start to use metabolic pathways typical for tumor cells (anaerobic
glycolysis) and actually become benign or malignant tumors (especially in liver).
20. How can we target cancer cells by using glycolysis?
 We can use deoxyglucose to stop the production of fructose-6-phosphate
 We can use 3-bromopyruvate to stop the production of 1,3-phosphoglycerate
 We can use dichloroacetate to induce switching of lactate back to pyruvate and to normal
metabolic activity
21. Why is AMP and not ADP used as a positive regulator of phosphofructokinase?
ATP can be still produced by combination of two ADP molecules, so it does not necessarily
indicate the lowest possible
22. What is the mnemonic for amino acids that can produce acetyl CoA
LLos Angeles PITT
Lysine, Leucine  Acetyl CoA  Phenylalanine, Tyrosine, Tryptophan
23. How do we define the energy charge?
Energy charge refers to the ratio of ATP/ADP – the cell is fully charged when all adenylate
nucleotide molecules are in the shape of ATP and discharged when they are in the shape of ADP.
24. Describe the structure of ATP channel
Two major proteins: F0 located in the membrane and F1 protruding to mitochondrial matrix.
Moreover, ATP synthase consist of stator formed by a, b, alpha, beta and delta molecules and
rotor made of c, e and gamma molecules. Flow of protons  rotor induces conformational change
 ATP synthesis takes place.
25. How NAD+ is regenerated in aerobic and anaerobic metabolic pathways
In aerobic pathway, NAD+ is regenerated during the electron transport chain and, in anaerobic
pathway, it is regenerated through conversion of pyruvate to lactate.
26. What is meant by electron transport potential?
Measure directly related redox potential of a compound which oxidization is used to produce ATP.
27. List components of electron transport chain
NADH-Q oxidoreductase
Q-cytochrome C oxidoreductase
Ubiquinol cytochrome C oxidoreductase
Cytochrome oxidase
28. Describe the action of glycerol phosphate shuttle
 Cytoplasmic glycerol-3-phosphate dehydrogenase converts dihydroxyacetone into
glycerol-3-phosphate, which then can be transported from cytoplasm to intermembrane
space
 There, glycerol-3-phosphate is converted again to dihydroxyacetone  it gives electrons
to FAD+ located in the matrix so FAD+ becomes FADH2 and can be used in the electron
transport chain
29. Describe the action of malate-oxaloacetate shuttle
 Aspartate is first converted to oxaloacetate in cytoplasm
 Then, oxaloacetate is converted to malate by using NADH from glycolysis
 Malate is transported to matrix, where it is changed into oxaloacetate and aspartate again,
giving NADH that can be used in electron transport chain
30. How do we measure phosphoryl transfer potential?
Through free energy change for the hydrolysis of ATP.
31. Which of the respiratory complexes do not pump hydrogen ions?
1+3=4
32. Explain the term standard electron potential and provide the equation that illustrates it. Also,
explain what is indicated by negative standard electron potential:
Standard electron potential can be defined as a measure of how readily X transfers electrons to
another molecule: X(g)  X+ (g) + e-. A negative standard electron demonstrates that X has
less affinity for electrons than H2.
33. Give the mnemonic used to describe which molecules are able to create a-ketoglutarate:
 PRO Arthur is Gentle to His Games
Proline, arginine, glutamine, histidine, glutamate
34. Describe the possible pathways of ingested glucose
1. Used as a storage  glycogen formed
2. Used for nucleotide synthesis and DNA repair  ribose-5-phosphate
3. Used as a quick but inefficient source of energy  pyruvate to lactate
4. Used as a more time-consuming but efficient source of energy  pyruvate
35. Describe the steps of pentose phosphate pathway
1. Glucose-6-phosphate is converted to 6-phosphogluconolactone by the enzyme glucose-
6-phosphate dehydrogenase
2. 6-phosphogluconolactone is converted to 6-phosphogluconate by the enzyme
phosphogluconolactase, which yields 1 NADH to be used by glutathione synthase
3. 6-phosphogluconate is converted to ribulose-5-phosphate by 6-phosphogluconate
reductase to give another NADH used in fatty acid synthesis
4. Ribulose-5-phosphate is converted by isomerase to ribose-5-phosphate
36. What type of bonding is found between dimers of lactose, maltose and sucrose?
Lactose: galactose-beta 1,4 – glucose
Maltose: glucose - alpha 1,4 – glucose
Sucrose: glucose – alpha 1, beta 2 – fructose
37. Electron transfer potential can be converted to…
Phosphoryl transfer potential.
38. What types of cells (beside tumor cells) require glucose as an energy source?
BERR mnemonic – brain, erythrocytes, retina, renal medulla
39. Outline glycolysis and its most important reactions
1. Glucose is converted to glucose-6-phosphate by hexokinase
2. Glucose-6-phosphate is converted to fructose-6-phosphate by phosphoglucoisomerase
3. Fructose-6-phosphate is converted to fructose-1,6-biphosphate by phosphofructokinase
4. Fructose-1,6-biphosphate breaks down to dihydroxyacetone and glyceraldehyde-3-
phosphate through action of aldolase
5. Glyceraldehyde-3-phosphate is converted to 1,3-biphosphoglycerate through action of
triose phosphate dehydrogenase
6. 1,3-biphosphoglycerate is converted to 3-phosphoglycerate by phosphoglycerokinase
7. 3-phosphoglycerate is converted to 2-phosphoglycerate through phosphoglyceromutase
8. 2-phosphoglycerate is converted to phosphoenolpyruvate through action of enolase
9. Phosphoenolpyruvate is converted to pyruvate through pyruvate kinase
40. Describe the stimulation and inhibition of the action of phosphofructokinase
1. Stimulated by AMP and fructose-2,6-biphosphate, which is produced by
phosphofructokinase-2 in state of hunger
2. Inhibited by ATP, citrate and accumulation of hydrogen ions
41. How do we calculate ATP yield from reactions?
ATP yield is the number of inorganic phosphate that is incorporated to form ATP per molecule of
oxygen used. ATP yield is 2.5 for oxidation of NADH and1.5 for oxidation of FADH2. The value
is influenced by uncoupling proteins.
42. What is needed to activate non-shivering thermogenesis?
Fatty acids for oxidation
43. What is the function of pyruvate dehydrogenase and the cause of its deficiency
Cause: X-linked condition, catalyzes the reaction of pyruvate and lipoamide into acetylated
dihydrolipoamide and carbon dioxide
44. 1 GTP molecule is generated during Krebs cycle. When?
When succinyl coA is being converted to succinate by succinyl coA dehydrogenase
45. Describe the pyruvate dehydrogenase complex
Pyruvate dehydrogenase complex is a complex of three enzymes that regulate oxidative
decarboxylation of pyruvate into acetyl CoA. It is allosterically regulated by phosphorylation an
D its activity determines glucose oxidation.
46. When two NADH + H molecules are being produced in the glycolysis
When glyceraldehyde-3-phosphate is being converted to 1,3-biphosphoglycerate by triose
phosphate dehydrogenase.
47. To which values is the standard energy change proportional?
The change in standard redox potential and the number of electrons transferred.
48. Explain how hydrogen ions contribute to ATP synthesis
1. Electron is transferred to ETC complex
2. The energy is used to transport hydrogen ion (with the formation of water as a by-product)
3. He hydrogen is attracted by negative electromagnetic field and flows through ATP
synthase channel to induce the reaction of ADP + Pi  ATP
49. State two differences between catabolism and anabolism
Catabolism is exorgenic and oxidative whereas anabolism is endorgenic and reductive.
50. Demonstrate the production of additional molecules during the step 1 and step 2 of
metabolism.
1. Fructose-1,6-biphosphate  pyruvate: 2ATP, NADH+H+ for each molecule
2. Pyruvate  Acetyl CoA  2 NADH+H for each molecule + CO2
3. Acetyl CoA  TCA cycle: 2CO2, FADH2, 3NADH + H+, GTP for each pyruvate
51. What are the substrates of fumarate?
Pardon, the fuck?
Phenylalanine, tyrosine  fumarate
52. Describe how pyruvate enters mitochondrion?
Transport of pyruvate into mitochondria occurs through pyruvate translocase (a symport with H+
ion). Then, the pyruvate can enter mitochondria and undergo process of oxidative carboxylation
in the mitochondrial matrix.
53. How is it possible that substrate binds to an active site?
Active site of enzymes contains two types of amino acids - the ones that allow catalytic activity
and the ones that allow specific binding between substrate and the enzyme.
54. Describe the Lineweaver Burke plot:
It is a double reciprocal plot so the x axis = 1/Substrate concentration and y axis = 1/V (mM/sec),
the x-intercept is -1/Km, the y-intercept is 1/Vmax and the slope is Km/Vmax. Km = Vmax
multiplied by slope of the line.
55. What is the pathology of von Hippel Lindau syndrome?
A person is deficient in prolyl hydroxylase which normally hydroxylates hypoxia inducing factor 
cell is not degraded and transcription factors are not muted when appropriate  patient is prone
to tumor development.
56. What are zygomens?
Zygomens are inactive precursors of enzymes that become activated when a covalent bond is
broken.
57. How methanol poisoning occurs? What is the treatment?
Methanol is converted to formaldehyde by the action of alcohol dehydrogenase, which causes
severe tissue damage and blindness. It is treated with 40% ethanol solution, as Km of ADH for
ethanol is 20 times lower than for methanol (higher affinity).
58. Describe how the following zygomens – trypsinogen, chymotrypsinogen and proelastase – are
converted tot heir active forms
1. Trypsinogen is converted to trypsin by the action of enteropeptidase
2. Chymotrypsinogen is converted to chymotrypsin by the action of trypsin
3. Proelastase is converted to elastase by the action of trypsin
59. Sum up irreversible competition in one sentence
It is always non-competitive and the covalent bonds of molecules are being broken.
60. How allosteric enzymes differ from the ones binding to the active site?
The V and S curve of allosteric enzymes have a sigmoidal shape when more substrate is added,
whereas substrates binding to the active site have a hyperbolic shape. Moreover, allosteric
enzymes can be controlled by allosteric inhibitors and allosteric activators.
61. Describe the cause and symptoms of von Gierke disease:
Cause  deficiency of glucose-6-phosphatase, so glucose-6-phosphate cannot be converted
back to glucose, appearance of glycogen is normal
Symptoms: severe fasting hypoglycemia, mouth and skin ulcers, bowel irritability, bacterial and
fungal infections, hepatomegaly, increase in blood lactate, triglycerides, uric acid and increase of
glycogen in liver. Treated with slow release glucose meals.
62. How we can measure Vmax and Km?
First, we measure the reaction at initial concentration known as V0, then plot the reaction velocity
at increasing substrate concentrations.
63. State three examples of coenzymes
NAD+, FAD+ and vitamin complexes
64. Give an example of why Km and Vmax matter
Prolyl hydroxylase – an enzyme responsible for hydroxylation of hypoxia inducing factor – has a
very high Km for oxygen, which enables it to monitor oxygen concentration over ranges of pO2
(be more sensitive).
65. What is a hemangioblastoma?
A benign, highly vascular tumor that occurs in brain, spinal cord and retina.
66. What are the units of Km and Vmax?
Units of Km = mM, units of Vmax = mM/s
67. What is the effect of temperature and pH change on enzyme?
Temperature results in vibrations that break bonds forming the structure of enzyme and pH
disrupts electrostatic attraction between molecules.
68. Describe the regulation of oxygen release by hemoglobin
Hemoglobin affinity for oxygen shows cooperative pattern. It is controlled by concentration of
hydrogen ion, CO2 and 2,3-biphosphoglycerate that is produced during the hypoxic conditions. It
has a higher affinity for deoxygenated hemoglobin, so it prevents binding of oxygen  more
oxygen can be released to the tissue.
69. Describe the nature of chymotrypsin and the reactions it catalyzes
Chymotrypsin, as well as trypsin, is not an allosteric enzyme, so its graph has a hyperbolic shape.
It catalyzes the breakage of peptide bonds in leucine, glutamate and histidine to produce acid and
amine, hydrolysis of ester bonds and cleavage of aromatic compounds.
70. Describe the mechanism of phosphorylation reactions
Phosphorylation reactions are reversible and are carried out by kinases to result in activation of
specific molecules. Amino acids that can form phosphate esters include serine, tyrosine and
threonine.
71. In what type of control is negative feedback inhibition used?
In allosteric control.
72. Give a clinical example of why Vmax and Km matter
Considering hexokinase and glucokinase: hexokinase is located in all tissues except liver, has a
very low Km  enables production of energy even if concentration of glucose is very low.
Glucokinase is present in liver and has a much higher Km to enable homeostasis and sensing of
glucose levels through wide ranges of its concentration.
73. What is MODY?
Maturity onset of diabetes in the young, which results in fasting hypoglycemia and is caused by
deficiency of GCK gene.
74. Give the equation for Km and explain its components
Km = k-1 + k2/all divided by k1. K-1 denotes the backwards rate of dissociation of enzyme-
substrate complex, k2 denotes the forward rate of the formation of the product and k1 denotes the
forward rate of formation of the enzyme-substrate complex.
75. Explain differences between different pancreatic proteases
All of these enzymes share the same mechanism of action but they differ in terms of compounds
on which they act:
 Trypsin – acts on basic amino acids such as lysine and arginine (Trying to fit is so basic)
 Chymotrypsin – acts on bulky side chains
 Elastase – acts on small and uncharged amino acids such as alanine, valine and threonine
76. List three examples of cofactors
 Zinc, iron and copper – responsible for redox reactions
77. From which product of the glycolysis pathway is the 2,3-BPG formed in hypoxic conditions?
 From 1,3BPG
78. Describe coenzymes
Coenzymes are a subgroup of cofactors (which can be also divided into inorganic molecules) that
can include molecules known as cosubstrates (transiently bound to protein) and prosthetic group
(strongly or even covalently bound to a protein).
79. What is the function of creatine kinase?
It transfers the phosphate from ATP to creatine in order to form phosphocreatine that serves as
an energy store in brain, muscles and heart.
80. What is the effect of the action of Hypoxia Inducing Factor?
Synthesis of red blood cells, formation of blood vessels and switching to aaerobic survival
pathways.
81. Define the term transition state
A state in which reactants have necessary energy and correct arrangements to form products of
the reaction.
82. Explain functioning of enzymes
Enzymes provide alternative reaction pathway with lower activation energy that enables the
establishment of transition state in which reactants have the highest free energy and correct
arrangement to form the products of the reaction.
83. Provide specific examples of active sites
Examples include three pancreatic serine proteases – called serine proteases because they all
contain reactive serine residues:
 Chymotrypsin has a hydrophobic active site that attracts bulky, aromatic compounds
 Trypsin contains negatively charged aspartate that attracts basic lysine, arginine and
histidine
 Elastase active site is partially blocked so it can only catalyze reactions with small and
uncharged molecules
84. Is allosteric inhibition the same as non-competitive inhibition?
No. All noncompetitive inhibition is allosteric inhibition, however, allosteric inhibition can also be
competitive (ex: it binds to allosteric site and covers the active site).
85. List four groups of partial proteolytic enzymes
Digestive enzymes: trypsin, chymotrypsin, carboxypeptidase A and B, phospholipase, elastase,
pepsin
Blood coagulation enzymes: VII IX X XI XIII + thrombin, kallikrein
Fibrinolytic enzymes: Plasminogen and plasminogen activator
Structural: Collagenase, chitin synthetase
86. List the conditions at which enzymes work
Body temperature, aqueous solution, near neutral pH
87. Do enzymes change the free energy required for the reaction?
No. Enzymes do not change the thermodynamic aspects of the reaction.
88. Categorize different types of inhibition of enzyme activity
First type of inhibition is reversible, which involves two types of inhibition: competitive (inhibitor
binds to the active site of enzyme and blocks it) and non-competitive (binds to the site other than
the active site and induces a conformational change that makes it unable to work). The other type
of inhibition is irreversible, which is always non-competitive.
89. Describe functioning of thiamine pyrophosphate?
Thiamine pyrophosphate is used as coenzyme in the metabolism of branched amino acids,
carbohydrates and fatty acids. Its precursors include pyruvate dehydrogenase, isocitrate
dehydrogenase, ketoacid dehydrogenase and a-ketoglutarate.
90. Describe the pathology of Monge’s disease (high-altitude disease)
Low partial pressure of oxygen leads to high level of erythrocytes in hematocrit and low levels of
oxygen in blood. When peritubular intestinal cells sense low pressure of oxygen, they induce the
production of erythropoietin, which results in formation of reticulocytes that later form mature
erythrocytes.
91. Define isozymes and give a specific definition of them
Isozymes are enzymes that differ in amino acid sequence but catalyze the same reaction. An
example is lactate dehydrogenase, which promotes anaerobic metabolism in muscles and aerobic
metabolism in heart.
92. Explain the pathology of Monge’s disease
1. Peritubular intestinal cells sense low concentration of oxygen  increased production of
erythropoietin
 2. Erythroblasts mature to reticulocytes
3. Reticulocytes mature to erythrocytes
93. What is the main manifestation of von Hippel Lindau syndrome?
Hemangioblastomas caused by deficiency of prolyl hydroxylase.
94. Give the equation for rate of reaction and describe how it implicates the order of reaction
Rate = Concentration of A to the power of f x Concentration of B to the power of q
F + Q = overall order of reaction, must be determined experimentally!
95. How isozymes relate to the activity of hypoxia inducing factor?
1. Cancer, stroke or heart disease  hypoxia
2. Hypoxia sensitive transcription factors are activated, causing the formation of LDHA gene,
which is responsible for dimer present in skeletal muscles
3. The dimer present in skeletal muscles incudes anaerobic glycosylation and other pathway
mechanisms
96. Provide an example when relative amounts of isozymes in body are significant for clinical
purposes
Creatine kinase is a dimer composed of two proteins - MM in skeletal muscles, MB in heart and
BB in brain. Presence of BB in blood indicates stroke or brain tumor and presence of MB indicates
cardiac arrest.
97. Describe aspartate transcarbamylase
Aspartate transcarbamylase is (as well as hemoglobin) an allosteric protein which catalyzes the
first step of the formation of cytidine triphosphate and uridine triphosphate, which are essential in
DNA and RNA production.
98. What is the main purpose of metal cofactors?
Stabilization of transition state and redox reactions
99. Describe steroid receptors
Steroid receptors are included in the family of transcription factors and are located in the
cytoplasm. When steroid hormones combine with them, it forms a steroid-receptor complex that
can bind to segment of DNA known as steroid-receptor element and cause transcription.
100. Describe what degenerate and unambiguous mean in reference to DNA molecule
Degenerate – one amino acid can be coded by different codons
Unambiguous – one codon can code for only one amino acid
101. Nucleotides are ____ of nucleosides
Phosphoric acid esters
102. Describe the tRNA structure
All tRNA are unique in their structure but they all share some common characteristics – D loop for
binding to aminoacyl-tRNA synthase, T loop for binding with ribosome, 3’ end with OH group for
binding with amino acid and 5’ end with phosphate group.
103. How RNA sugar differs form that from DNA?
It has OH on the second carbohydrate.
104. How do we number carbons in sugar molecule of DNA/RNA?
We start form the carbon attached to the nucleotide.
105. How phosphodiester bond is formed?
It is formed between OH on the third carbon molecule of nucleotide sugar and phosphorus located
on the 5th end of another nucleotide sugar. OH molecule acts as a nucleophile and attacks
phosphorus.
106. What is the difference between prokaryotic and eukaryotic ribosomes?
Eukaryotic ribosomes contain 4 subunits (including 5.8S) whereas prokaryotic contain 3 subunits.
107. Describe features of DNA replication and how it differs between eukaryotes and
prokaryotes:
DNA replication is semi-conservative, bi-directional and uses DNA polymerase that cannot
synthesize a primer on its own (needs a DNA primase). In eukaryotes, replication has many points
of origin,
108. Describe the structure and functioning of aminoacyl-tRNA synthetase
They have structure which is highly specific for tRNA and amino acid, use energy from ATP and
release pyrophosphate that can be further used in the synthesis of amino acid sequence.
109. What are the building blocks of DNA and RNA
RNA – ATP, UTP, CTP, GTP – add deoxy- to obtain the ones used for DNA.
110. What are the differences between DNA and RNA polymerase?
 DNA polymerase has a 3’5’ proofreading activity
 DNA polymerase requires a primer
 Substrates for DNA polymerase include dioxynucleoside triphosphates
111. Describe the initiation of translation
Initiation of translation requires GTP and IF. A small ribosomal subunit binds to the 5’ end of mRNA
and slides until it finds AUG codon. When it is found, tRNA carrying methionine binds its anticodon,
large ribosomal subunit is assembled  tRNA ends up being in the P site.
112. What is a point mutation and what are its subtypes?
Point mutation occurs when single base is replaced in DNA. It has three subtypes: missense,
nonsense and silent. Silent = no change, missense = change in amino acid, nonsense = early
STOP codon.
113. What happens with the protein that is already translated?
Might noT be endeD.
Modification – addition of functional group, Translocation – moving protein to its cellular
destination which is dependent on amino acid contained within the protein, Degradation
114. What is the cause of hereditary emphysema?
Misfolding of a-antitrypsin inside ER.
115. Give examples of post-translational modification
Glycosylation, proteolysis, phosphorylation, specific proteolytic cleavage in ER, formation of
disulfide bonds, assembly of multisubunit complex
116. Describe initiation of transcription
1. TBP – TATA binding protein
2. Transcription factors associate
3. DNA Polymerase also binds II
4. Other transcription factors also associate
117. Describe the processing of pre-mRNA
7-methylguanosine phosphate is added to the 5’end, poly-A tail is formed at the 3’end and the
spliceosome is used to transform the formed hnRNA molecule into mRNA by cutting out introns.
118. Describe the three-dimensional structure of tRNA
Has an L-shaped conformation, in which stem is hydrogen bonded and loops are not hydrogen
bonded.
119. What are the locations to which bound ribosome is transported?
 P BEGS T
P – plasma membrane, B - bonded, E – ER, G – Golgi apparatus, S – secretion, T –
translocated co-translationally
120. Describe the organization of genetic material in the nucleus
DNA is wound around 8 histone proteins to form an octamer, which is the structural unit of
nucleosome. The proteins have positively charged side chains and are attracted to the negatively
charged phosphate of DNA structure. Nucleosomes form fiber called chromatin which itself can
assemble to form chromosomes.
121. In which direction does the DNA polymerase move?
From 3’ to 5’ end (because it catalyzes formation of the strand that is from 5’ to 3’ end).
122. Why silent mutations exist?
Because genetic code is degenerate.
123. What antiretroviral medication can be used in HIV/AIDS
Zidovudine (known as azidothymidine) does not contain 3’ OH group, so it terminates the
formation of viral DNA. It works because viral reverse transcriptase has a higher affinity for
zidovudine than DNA polymerase does.
124. Describe the role of TBP in transcription
It associates with promoter region in the TATA box of the gene and recruits other factors to begin
transcription as it introduces a kink in the DNA molecule. It is required by all DNA polymerase II
transcribed genes.
125. Describe pathophysiology of I-cell disease
Proteins are not marked with mannose-6-phosphate  are not secreted to lysosomes  become
clogged up in the cell and lysosomes cannot properly digest material  death before the age of
8.
126. Describe the termination of transcription
RNA forms a stem-loop structure followed by stretch of uracil, specific enzymes cleaves it, RNA
is released and polymerase dissociated
127. Describe the sequence of initiation factors involved in translation:
Ternary complex is formed by GTP, eIF2 and tRNA. It then forms preinitiation complex with eIF3,
eIF5, eIF1, eIF1A and small ribosomal subunit. Finally, the complex is directed to the 5’ end of
DNA with eIF-4F ribosomal subunit.
128. Which enzyme catalyzes the formation of peptide bond between the translated amino
acids?
Peptidyl transferase – it also hydrolyzes the bond between tRNA and final amino acid (with help
of release factors).
129. Free ribosomes make proteins destined for:
Mitochondria, nucleus and cytosol, are translocated after translation.
130. What is the source of phosphate in replication?
dXTP nucleotides  one phosphate is used to from bond between nucleotides, the other two
phosphates are used as an energy source for later
131. Describe how DNA nucleotide excision works
A form of repair when DNA is damaged by, for example, UV light. ABC exonuclease removes the
nucleotides from DNA strand, DNA Polymerase I adds new nucleotides and DNA ligase seals the
gap.
132. Describe how DNA base excision works
 1. Damaged base is removed by DNA glycosylase, which leaves AP site
2. AP endonuclease removes the sugar and phosphate
3. AP excision endonuclease removes several more bases
133. Which enzymes are used in eukaryotic transcription?
 DNA polymerase alpha and delta form the tRNA strand
 RNase 5 removes RNA from primer
 DNA polymerase delta replaces RNA from primer with DNA
134. Processing – to what does it refer?
To the formation of mRNA from pre-mRNA
135. Explain how mismatch repair works
Mut proteins bind to mismatched region and recruit Polymerase I which removes mismatched
base and surrounding bases.
136. What are the 4 types of chromosomal mutations?
Deletions, duplications, inversions and translocations
137. Describe the termination of translation
When ribosome encounters STOP codon, there is no aminoacyl-tRNA that codes for it. Therefore,
release factor binds to stop codon, and, by using energy from GTP hydrolysis, allows amino acid
to be released from ribosome.
138. Describe components of promoter
TATA box, DNA, initiation site for transcription
139. Insertion mutation can lead to which mutations?
Splice site mutation and Frameshift mutation
140. Proofreading refers to the…
Removal of incorrect nucleotides immediately after they are added to the DNA chain during
replication.
141. Why DNA replication is discontinuous?
DNA polymerase can add nucleotides only to free 3’ end, which is present in the leading strand
but not present in the lagging strand
142. Describe the elongation of translation
Elongation factor EF1a binds tRNA to the A site and is released by GTP hydrolysis. Then, EFbp
regenerates EF1a. EF2 moves ribosome along the mRNA by one codon.
143. Describe regulation of gene expression
Gene expression is regulated by transcription factors, which are DNA-binding proteins consisting
of two domains: DNA-binding domain and transcriptional activity domain. They bind to specific
DNA sequences close to promoter – such as enhancer – and regulate transcription either
positively or negatively.
144. Describe RNA polymerases
They are multisubunit complexes, there is only one present in prokaryotes and I II and III present
in eukaryotes (II transcribes all DNA), they can be recognized by their sensitivity to alpha-amanitin
(a toxin which is selective inhibitor of DNA polymerase II and III).
145. Explain the difference between driver and passenger mutation
Driver mutations are the ones that contribute to cancer. Passenger mutations result in formation
of unstable tumor but they themselves do not contribute to cancer. It is important to realize that
driver mutations and not the tissue of origin determine the characteristic of cancer.
146. What are the two types of nucleotide excision repair?
Global genome NER repairs damage in both transcriptionally active and inactive DNA, whereas
transcription coupled ENR repairs damage in transcriptionally active DNA only.
147. Describe the pathophysiology of melanoma
Normal cascade: NRAS  BRAF MEK  ERK, regulates cell growth, differentiation and
survival. In case of mutant BRAF or NRAS, the pathway becomes bypassed  results in
melanoma.
148. What is the possible medication for melanoma and its action?
Vemurafenib  Inhibits BRAF.
149. Describe interphase
Interphase includes G0 G1 G2 and S  cell grows, normal metabolic activity, DNA replicates.
150. A DNA double strand break cannot be repair. Which gene might be mutated?
RAD51.
151. Which condition occurs due to mismatched pair?
Hereditary Colorectal cancer
152. What is the distribution for the risk of cancer?
Cancer has a normal bell-shaped curve because it is a multifactorial condition (disease of
mosaicism) rather than high-penetrance Mendelian disorder
153. What is retinoblastoma?
Retinoblastoma is a tumor suppressor gene that can become dysregulated when cells with two
altered copies of BR1 gene produce no functional retinoblastoma protein and are unable to
regulate the cell cycle. It is usually autosomal dominant but has variable penetrance as not every
person with mutation has the disease.
154. How to produce thymine from cytosine?
Cytosine has to undergo methylation in order to form 5-methylcytosine and then deamination in
order to form thymine.
155. What is a central dogma?
Central dogma describes the two-step process that includes transcription and translation, which
enables the conversion of genetic material to a functional protein.
156. Which stage of the cell cycle is the stage in which cell is just a cell (but is very metabolically
active?)
G0 stage
157. Which genes might be responsible for the formation of cancer?
Two groups  oncogenes if turned on and tumor suppressor genes if turned off + DNA repair
genes (turned off) or genes responsible for metabolism (if dysregulated) because they cannot
metabolize carcinogens
158. Describe the Hannah and Weinberg hallmarks of cancer
E-LISTS
E – evading apoptosis
L – limitless replicative potential
I – insensitivity to growth-restraining strands
S – self-sustained growth factors
T – tissue metastasis
S – sustained angiogenesis
159. Describe two-hit hypothesis
As most of the loss-of-function mutations of the tumor suppressor genes are recessive, both of
the genes must be mutated in order to result in a condition.
160. DNA methylation
Addition of the methyl group to the 5’C carbon of the cytosine that occurs before guanine, affected
by environment, might result in mutations from cytosine to thymine. Causes gene silencing in
cancer and, as well as deacetylation, is a target of drug therapy.
161. How do you define a contaminant?
Contaminant is an organism that grows in bacterial culture by accident
162. Give the definition of capnophilic
Capnophilic organism is the one which prefers high carbon dioxide concentration in environment
163. Give examples of gram-positive bacteria:
Streptococcus, Staphylococcus, Enterococcus, Clostridium, Fusobacterium
164. How do we define virulence?
Virulence is the capacity of an organism to cause damage to the host, which can be expressed as
number of deaths (y-axis) per number of organisms from strain given per unit of time (x-axis).
165. Describe spore formation
1. DNA is replicated and aligns along cell’s long axis
2. Cytoplasmic membrane invaginates to form forespore (binary fission)
3. Second membrane engulfs the forespore, second vegetative DNA degenerates in thw
meantime
4. A cortex of calcium and dipcolinic acid is formed around the endospore
5. Endospore is released by cell lysis
166. Give names of classes of different Staphylococci
 Aureus
 Epidermidis
 Saprophiticus
 Lugdunesis
 Schleiferi
167. Describe systemic inflammatory response syndrome
Inflammatory response syndrome is caused by endotoxins (lipopolysaccharides) and
peptidoglycans located on the bacterial wall and exotoxins combined with superantigen (TSS-1)
molecules. Endotoxins activate macrophages whereas exotoxins activate T-cells. Inflammatory
response syndrome results in release of pro-inflammatory cytokines.
168. What components of bacterial wall can result in inflammation?
 Endotoxins – lipopolysaccharides located on the outer wall of bacteria, which bind to
receptors of macrophages and B cells to stimulate the release of acute phase proteins
 Lipoteichoic acid
 Lipoproteins
 Peptidoglycans
169. Why patients with coliform (negative) sepsis quickly become unwell?
Because of the endotoxin released from the bacterial cells when they die.
170. Describe features of coliform bacteria
 Gram-negative
 Anaerobic or aerobic
  Many of them are a part of normal bacterial flora (normal inhabitants of intestinal tract, ex:
E. Coli)
 Ferment lactose
 Can be differentiated by antigenic structure and their wall
 Bacilli
171. Describe the unique elements of structure of gram-negative bacteria
1. Lipopolysaccharide located on the outer membrane
2. Peptidoglycan covering the inner membrane
172. Discuss the classification of Streptococcus species
Streptococcus species are classified on the basis of hemolysis. Beta-hemolytic species contribute
to complete hemolysis of blood cells on blood agar and result in a brown trace. Alpha-hemolytic
species contribute to partial hemolysis and result in a green trac (which can be also caused by
change of hemoglobin to methemoglobin caused by hydrogen peroxide). Finally, gamma-
hemolytic species cause no hemolysis. Lancefield method can be used to further group alpha and
beta hemolytic species on the basis of their cell wall polysaccharide.
173. Discuss the infection by S. aureus
S. aureus is a gram-positive, beta-hemolytic cocci bacteria, which is a facultative anaerobe. Origin
of its infection is usually nosocomial or community-based, as the bacteria is resistant to penicillin
and can become resistant to methicillin. It invades nasal nares and perineum and leads to toxic
shock syndrome, pneumonia and skin infections. It can be treated with penicillinase-resistant
penicillin or vancomycin.
174. Describe mechanism of fever production caused by endotoxins
Endotoxins bind to receptors of macrophages, which, in turn, release cytokines that travel to
anterior hypothalamus and result in adverse septic response. Prostaglandin E is then released
and raises body’s thermal set point, so the environment is perceived as too cold and person starts
to shiver in order to conserve heat.
174. What are the other methods (aside from spectrometry) that can be used to classify
bacteria?
16S RNA sequencing and qPCR
175. What is the first line of treatment of infections caused by coliforms?
Gentamicin
176. Describe Clostridium species
Clostridium is a gram-positive bacillus, which is a normal part of bowel flora in humans and animals
and can be found in feces. It produces endotoxins that cause severe damage and spores that can
survive for many months. There are two main types of clostridium – clostridium difficle, which
causes antibiotic-associated diarrhea in elderly and clostridium perfringens, which causes gas
gangrene – a soft tissue damage following contamination of wound. Clostridium tetani causes
tetanus.
177. What is pneumonia?
Pneumonia is the inflammation of the lungs caused by Streptococcus pneumoniae, which results
in accumulation of fibrous exudate in the lungs.
178. Explain how serologic test are used in microbiology
Detects IgM antibodies produced for specific antigen of virus of bacteria, which identity can be
confirmed through in vitro aggregation reaction.
179. Describe Streptococcus pneumoniae
Gram-positive bacteria with short chains, they are a normal part of human respiratory tract flora,
the most common cause of pneumonia, they can cause meningitis as well. Majority of UK forms
are still sensitive to penicillin.
180. List advantages and disadvantages of MALDI TOF technique
 CO-R-PPO  COst-effective, rapid, precise, POwerful.
 Disadvantage: not good for streptococci and staphylococci
181. Provide two examples of fungal infections:
Candida – result in yeast budding, result from skin infection and lead to candidemia
Aspergillus – causes aspergillosis, an infection in which fungus colonizes (usually) lungs, common
in the immunocompromised
182. List bacteria normally associated with gut flora
Non-pathologic commensal coliforms: E.coli, Klebsiella, Enterobacter, Proteus
Pathologic forms: Shigella, Salmonella, Verotoxin-producing E. Coli O157 and O104
183. List gram-negative bacteria
PS SEEK Pro BaN H:
 Pseudomonia
 Salmonella
 Shigella
 Enterobacter
 Escherichia
 Klebsiella
 Proteus
 Bacteroides
 Neisseria
 Hemophilus
184. Explain multilocus sequence typing technique
PCR  followed by DNA sequencing  allows to discriminate among strains of bacteria on the
basis of differences in alleles (present in created allelic profiles)
185. What is the difference between exogenous and endogenous organisms
Exogenous organisms are the ones not normally present in specific flora, whereas endogenous
are the ones that are usually present. Both endogenous and exogenous organisms constitute
microbiota.
186. What is a microbiome?
Microbiome is the entire genetic material of microbiota, which, in turn, includes all organisms
present in a specific niche.
187. What are the group A streptococci?
A species of gram-positive Streptococcus pyrogen bacteria that have Lancefield group A antigen
and beta-hemolytic activity. They cause necrotizing fasciitis, puerperal sepsis and Scarlet fever
188. What are the unique elements of gram-positive bacteria?
Multilayered peptidoglycan found on the cell membrane.
189. Describe the occurrence of sepsis
Sepsis causes tiny blood vessels to become leaky  more fluid is transported to tissues. The
lowered volume of blood results in more rapid heart rate and is accompanied by lower oxygen
perfusion to tissues, so blood supply to organs less essential than brain is cut. Clotting factors
are used to create clots within tiny blood vessels, however, if they are used up, the risk of
hemorrhage increases.
190. Explain how to prepare a gram stain
1. Prepare heat-fixed film of bacteria
2. Stain with crystal violet for one minute and rinse with water
3. Stain with gram’s iodine for one minute and rinse with water
4. Clean with acetone or ethanol
5. Stain with fuchsin or safranin for 1 minute and rinse with water
6. Blot dry and compare both samples under oil immersion. Positive gram should be pink
(do not retain crystal violet) and negative gram should be blue/violet.
191. Explain Ziehl Nelson staining
192. Fluorochromes
193. Which drugs are sued to combat gonorrhea?
Azithomycin, doxycycline and cephalosporin
194. What is the source and targets of MRSA?
Source – mainly nosocomial, intensive car units.
Targets – immunocompromised patients, burns patients, dialysis patients, elderly, surgical
patients.
195. Give examples of two selective media
MSS – Mannitol salt agar: 7.5% salt to allow isolation of Staphylococci
SS – Shigella-Salmonella agar: introduction of bile salts to prevent formation of positive-gram
coliforms and Proteus
196. What diseases are caused by Neisseria?
STD, STI and meningitis
197. What are protozoans? What disease do they cause?
Protozoans are single-celled eukaryotic organisms that can be parasitic. Examples of parasitic
protozoans include: Malaria, Entamoeba, Leishmaniasis, Toxoplasma (MELT), Cryptosporidium
198. Describe fusobacterium
Fusobacterium are gram-negative bacteria that do not produce spores and have a slim bacilli.
They include F. nucleatum and polymorphum.
199. How to differentiate between pyogenic and millleri Sreptococcus?
Pyogenic have bigger colonies.
200. Name three examples of gram-positive bacteria and the diseases they cause
1. Streptococcus – pneumonia, GAS infections, strep throat
2. Enterococcus – enteric infections
3. Staphylococcus – anaerobic bacilli, nosocomial and community, cause skin infections
4. Clostridia
201. Give two examples of gram-negative cocci
Neisseria meningitis and Neisseria gonorrhea
202. Coliforms can cause:
 Urinary tract infection
 Peritoneum inflammation
 Biliary tract infection
203. Describe Staphylococci
Gram-positive non-motile bacteria that are aerobic (facultative anaerobic too), catalase oxidase
and coagulase positive (also coagulase negative)
204. Describe Clostridium difficle
Occurs due to antibiotic therapy, is responsible for pseudomembrane colitis.
205. What is the role of neutralizing antibodies in viral infections?
Neutralizing antibodies include IgM and IgG, they prevent virus from binding to cellular receptors
and are more important in humoral immunity
206. List viruses and cancers that are related to them:
Human papilloma virus: cervical cancer
Hepatitis B and C virus: primary hepatocellular carcinoma
Epstein Barr virus: lymphoma and leukemia
Human herpes virus: Kaposi’s sarcoma
Helicobacter pylori: gastric cancer
207. Describe adenovirus
Conjunctivitis, pharyngitis, diarrhea and pneumonia
Has icosahedral symmetry
208. Describe persistent viral infections
Persistent infections are usually intermittent, with periods of increased activity combined with
periods of latency - an example is herpes simplex virus and varicella-zoster virus. They can also
remain active for many years – an example for that is HIV or Hepatitis C.
209. What is the target of erythromycin and what is the target of penicillin?
Erythromycin acts on ribosomes, whereas penicillin acts on cell walls of bacteria.
210. How do viruses enter the cell?
Either through fusion of viral membrane and cell membrane or through endocytosis, in which
binding of receptor initiates internalization of the virus into the cell.
211. Give examples of viruses that can infect individuals, however, they might show no
symptoms of the disease
Rhinovirus, poliovirus, TTV
212. Explain tissue tropism
Tissue tropism refers to the support of growth of a particular virus or bacterium. Some bacteria
and viruses have a broad tissue tropism and can infect many types of cells and tissues.
213. List conditions associated with herpes virus
Oral herpes, genital herpes and herpes encephalitis
214. Define antimicrobials
Drugs that can be used to treat infections that are bacterial, fungal, viral or protozoal
215. Describe methods in which virus can be detected
PCR combined with mass spectrometry, antigen detection and older techniques such as cell
culture or electron microscopy
216. What proteins are the target of viral drugs?
Integrase and protease – integrase forms covalent bonds between host’s DNA and viral DNA
and protease that severe peptide bonds of amino acids.
217. How immune system reacts to viral RNA?
It becomes a ligand for toll-like receptor 3, which, in turn, leads to a release of interferons
218. What is a lipopolysaccharide?
A type of glycolipid located on the outside cell membrane of gram-negative bacteria, it is
composed of lipid A, polysaccharide and O-chain.
219. Describe the two newly proposed domains of life
Bacteria and Archaea that give rise to Eukarya. Archaea also include TACK: (all end in cheota):
thaumar, algar, crenear, korar
220. What are the four phases of bacterial growth?
Lag phase, exponential phase, stationary phase and decline phase
221. Describe the composition of cell wall in bacteria:
Both gram negative and gram positive are composed of peptidoglycan, which has altering sugar
residues of B-1,4-linked N-acetylglucosamine and N-acetylmuramic acid.
222. Describe the additional components of bacterial cells:
Flagella composed of flagellin that are found in both gram positive and gram negative bacteria
as well as pilus found only in gram negative bacteria and fimbriae found only in positive gram
bacteria.
223. What are types of pili?
I - rigid with flexible adhesin, found in E.coli, IV – flexible with two pili proteins, E. coli, Neisseria,
Pseudomonas, curli phili – E.coli, coiled, aggregative fragment, have 2 pili proteins
224. Describe components of bacterial cell
Cytoplasmic or plasma membrane – they can be destroyed by using sonication or ethanol
Cell wall – target of penicillin, chromosome – gyrase is a target of quinolones, ribosome –
erythromycin
225. List antibiotics that target protein synthesis
aminoglycosides, tetracyclines, macrolids, fusidic acid, lincosamide,
chloramphenicol
226. How do beta-lactamases work?
They bind to DD-transpeptidase and block the cell wall synthesis. They include penicillin and
cephalosporins, which can both contain clavuclanic acid that is an inhibitor of beta-lactamase
present in some bacteria.
227. What are tetracyclines?
They are type of antimicrobials that target protein synthesis by binding to 30S ribosomal subunit
and preventing tRNA from binding to the ribosome. They have a wide spectrum of action – an
example of bacteria on which they act is Chlamydia.
228. What are lincosamides?
They are antimicrobials that bind to the 50S part of protein and thus inhibit protein synthesis. An
example of lincosamide is clindamycin.
229. Describe drugs that have an effect on protein synthesis
They include macrolides and gentamicin – all are bacteriostatic.
230. What infections can be caused by coliforms
Urinary tract infection, peritonitis, biliary tract infection
231. Name 5 examples of gram-positive pathogens
Streptococcus, Staphylococcus, Clostridium, Enterobacterium, Fusobacterium
232. Gram negative prokaryotic pathogens
Neisseria, E. coli, Enterobacter, Pseudomonas, Proteus, Hemophilus, Bacteroides, Salmonella,
Shigella, Klebsiella, Bacteroid
233. Which antibiotics should be avoided due to their association with Clostridium infection?
Cephalosporin, Co-amoxiclav, Clindamycin, Ciprofloxacin
234. State main classes and examples of antimicrobials
 The ones that inhibit cell wall synthesis - beta lactams and glycopeptides
  The ones that inhibit protein synthesis – three classes – first: macrolides (erythromycin,
clarithromycin, azithromycin), second class: gentamicin, third class – tetracyclines,
chloramphenicol, doxycycline, clindamycin
 Inhibit acid synthesis: Metronidazole, trimethoprim, fluoroquinolones
235. Metronidazole
Breaks strands of bacteria and protozoa, can be given orally or intravenously, resistance is rare,
might cause furred tongue and metallic taste.