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Biochemistry Orals
Biochemistry Orals
EXAM PDF
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01. Common properties of enzymes and inorganic
catalysts. The specific properties of enzymes.
• Catalyze only thermodynamically possible reactions
• Are not used or changed during the reaction.
• Don’t change the position of equilibrium and
direction of the reaction
• Usually act by forming a transient complex with the
reactant, thus stabilizing the transition state
Specific properties of enzymes:
• 1. Accelerate reactions in much higher degree than
inorganic catalysts
• 2. Specificity of action
• 3. Sensitivity to temperature
• 4. Sensitivity to pH
02. The structure of simple and complex enzymes.
• regulatory properties,
released.
Examples of High-energy compounds:
➢ Phosphoenol Pyruvate[PEP]
➢ 1,3- diphosphoglycerate
➢ Creatine phosphate
032. Ways of ATP formation in the organism: substrate-
level and oxidative phosphorylation reactions.
There are 2 ways of ATP formation in the organism:
oxidative phosphorylation and substrate-level
phosphorylation. Oxidative phosphorylation is the
formation of ATP from ADP and phosphate at the
expense of the energy yielded by electron transport to
oxygen.
Substrate-level phosphorylation is the formation of ATP
from ADP and phosphate group donated by certain
substrates.
033. Tissue respiration: location in the cell, sequence of
reaction.
Tissue respiration is the release of energy, usually from
glucose, in the tissues of all animals, green plants, fungi
and bacteria. All these living things require energy for
other processes such as growth, movement, sensitivity,
and reproduction. The most efficient form of respiration
is aerobic respiration: this requires oxygen. When
oxygen is not available, some organisms can respire
anaerobically i.e. without air or oxygen. Yeast can
respire in both ways. Yeast gets more energy from
aerobic respiration, but when it runs out of oxygen it
does not die. It can continue to respire anaerobically,
but it does not get so much energy from the sugar. Yeast
produces ethanol (alcohol) when it respires
anaerobically and ultimately the ethanol will kill the
yeast
complex II - succinate-CоQ-reductase.
Transfers electrons from succinate to Co Q.
Form 1 consist of:
- enzyme succinate dehydrogenase (FAD – prosthetic
group)
- iron-sulfur clusters.
Succinate reduces FAD to FADH2 . Then electrons pass to
Fe-S proteins which reduce Q to QH2.
Complex II does not contribute to proton gradient.
035. Molecular complexes of inner mitochondrial
membranes:
complex III - CоQ- cyt.с1- reductase.
Transfers electrons from ubiquinol to cytochrome C.
Consist of:
cytochrome b,
Fe-S clusters and cytochrome c1 .
Cytochromes – electron transferring proteins containing a
heme prosthetic group (Fe2+ Fe3+).
Oxidation of one QH2 is accompanied by the translocation
of 4 H+ across the inner mitochondrial membrane. Two
H+ are from the matrix, two from QH2.
complex IV - cyt. с – oxidase.
Transfers electrons from cytochrome c to O2 .
Composed of: cytochromes a and a3 .
Catalyzes a four-electron reduction of molecular oxygen
(O2 ) to water (H2O):
O2 + 4e- + 4H+ → 2H2O
Translocates 2H+ into the intermembrane space.
Cytochrome c oxidase consists of 13 subunits and contains
two hemes (two iron atom) and three copper ions,
arranged as two copper centers.
Cytochrome c oxidase pumps four additional protons from
the matrix to the cytoplasmic side of the membrane in
the course of each reaction cycle (mechanism under
study). Totally eight protons are removed from the
matrix in one reaction cycle (4 electrons).
036. Mitchell's chemiosmotic theory.
➢ electron transport and ATP synthesis are coupled
by a proton gradient across the inner mitochondrial
membrane.
➢ Mitchell's chemiosmotic hypothesis was the basis
for understanding the actual process of oxidative
phosphorylation.
Mitchell’s postulates for chemiosmotic theory
1. Intact inner mitochondrial membrane is required.
2. Electron transport through the ETC generates a
proton gradient 3. ATP synthase catalyzes the
phosphorylation of ADP in a reaction driven by
movement of H+ across the inner membrane into
the matrix.
037. Oxidative phosphorylation, mechanism of H+ -ATP-
ase operation.
➢ Oxidative phosphorylation is the process in which ATP
is formed as a result of the transfer of electrons from
NADH or FADH2 to O2 by a series of electron carriers.
➢ The H+ -ATP-ase found in vacuoles of the eukaryote
cell cytoplasm is similar to the archaeal enzyme, and
is thought to reflect the origin from an archaeal
ancestor.
➢ In most systems, the ATP synthase sits in the
membrane (the "coupling" membrane), and catalyses
the synthesis of ATP from ADP and phosphate driven
by a flux of protons across the membrane down the
proton gradient generated by electron transfer.
➢ The flux goes from the protochemically positive (P)
side (high proton electrochemical potential) to the
protochemically negative (N) side. The reaction
catalyzed by ATP synthase is fully reversible, so ATP
hydrolysis generates a proton gradient by a reversal
of this flux.
➢ In some bacteria, the main function is to operate in
the ATP hydrolysis direction, using ATP generated by
fermentative metabolism to provide a proton
gradient to drive substrate accumulation, and
maintain ionic balance.
ADP + Pi + nH+ P <=> ATP + nH+n
038. Inhibitors of tissue respiration.
Rotenone and barbiturate drug, amytal block electron
transfer in Complex I.
➢ Rotenone is insecticide that strongly inhibits the
electron transport of complex I.
➢ Rotenone is a natural product obtained from the
roots of several species of plants.
Amytal is a barbiturate drug that blocks electron transport
from NADH to coenzyme Q
2 – Thenoyltrifluoroacetone and carboxin specifically block
electron transport in Complex II.
Antimycin A interferes with electron flow through Complex
III.
➢ Antibiotic.
➢ Induces apoptosis.
➢ Inhibits mitochondrial electron transport
specifically between cytochromes b and c.
Cyanide, azide, and carbon monoxide block electron flow in
Complex IV.
➢ Azide and cyanide bind to the iron when the
iron is in the ferric state.
➢ Carbon monoxide binds to the iron when it is
in the ferrous state.
➢ Cyanide and azide are potent inhibitors at this
site which accounts for there acute toxicity.
➢ Carbon monoxide is toxic due to its affinity for
the heme iron of hemoglobin.
➢ Carbon monoxide binds to cytochrome a/a3
but less tightly than cyanide.
➢ It also binds to hemoglobin, displacing oxygen.
➢ Symptoms include headache, nausea,
tachycardia, and tachypnea.
➢ Lips and cheeks turn a cherryred color.
➢ Respiratory depression and coma result in
death if not treated by giving oxygen.
➢ Sources of carbon monoxide include:
• Propane heaters and gas grills
• Vehicle exhaust
• Tobacco smoke
• House fires
• Methylene chloride–based paint strippers
Other inhibitors include antimycin (cytochrome
b/c1), doxorubicin (CoQ), and oligomycin (F0).
039. Uncoupling agents of oxidative phosphorylation.
➢ Uncouplers are lipid-soluble aromatic weak acids
➢ Uncouplers deplete proton gradient by
transporting protons across the membrane
2,4-Dinitrophenol
➢ 2,4-Dinitrophenol permeabilizes the inner
mitochondrial membrane to protons, destroying
the proton gradient and uncouples the electron
transport system from the oxidative
phosphorylation.
➢ In this situation, electrons continue to pass through
the electron transport system and reduce oxygen
to water, but ATP is not synthesized in the process.
Valinomycin
➢ combines with K ions to form a complex that passes
through the inner mitochondrial membrane.
➢ As a proton is translocated out by electron transfer,
a K ion moves in, and the potential across the
membrane is lost.
➢ This reduces the yield of ATP per mole of protons
flowing through ATP synthase (FoF1). In result -
electron transfer and phosphorrylation become
uncoupled.
➢ Valinomycin is a potent antibiotic which acts as a
potassium (K+) ionophor.
Oligomycin
➢ ATP synthase is inhibited by oligomycin which
prevent the influx of protons through ATP
synthase.
➢ Oligomycin is a natural antibiotic isolated from
Streptomyces diastatochromogenes which inhibits
mitochondrial H+-ATP synthase.
➢ It is primarily found to act as an inhibitor of
mitochondrial respiration.
➢ This binding blocks the proton conductance and
inhibits the synthesis of mitochondrial ATP.
040. Oxygen radicals. Free radicals oxidation.
➢ A free radical is any atom or molecule that contains
one or more unpaired electrons.
➢ The unpaired electrons alter the chemical reactivity
of an atom or molecule, usually making it more
reactive than the corresponding non-radical.
➢ Free radicals can originate endogenously from
normal metabolic reactions or exogenously as
components of tobacco smoke and air pollutants
and indirectly through the metabolism of certain
solvents, drugs, and pesticides as well as through
exposure to radiation.
➢ The process of damage by free radicals is called
free radical oxidation.
➢ A free radical is stopped when the electron
difference (gaining or losing an electron) is
corrected.
➢ Molecules that can correct the electron difference
are called - Antioxidants.
➢ Antioxidants are found in dark colored vegetables
and fruit and in dietary supplements.
Oxygen radicals
single electron - superoxide anion (O2 -1)
two electrons – peroxide (O2 -2).
➢ O2 .-, O2 2- and, particularly, their reaction
products are harmful to cell components - reactive
oxygen species or ROS.
041. Classification and representatives of carbohydrates.
042. Digestion of carbohydrates: localization, types,
role of enzymes.
➢ The process of digestion starts in the mouth by the
salivary enzyme –amilase. .
➢ The time for digestion in mouth is limited.
➢ Starch in mouth: hydrolyzed by salivary alfa-amylase
into Maltotriose, Dextrin, Maltose
➢ Starch contain : alfa-1,4-glucosidic linkages and
branched chains alfa-1,6 linkages (branch points,
amylopectin) Alfa-amylase: present in saliva and
pancreatic juice.
➢ Specific for internal alfa-1,4-glucosidic bonds
➢ Salivary -amilase is inhibited in stomach due to the
action of hydrochloric acid.
➢ Another -amilase is produced in pancreas and is
available in the intestine
➢ -amilase hydrolyzes the -1-4-glycosidic bonds
randomly to produce smaller subunits like maltose,
dextrines and unbranched oligosaccharides.
➢ -1-6-glycosidic bonds hydrolyze oligo-1,6- glycosidase
➢ The intestinal juice contains enzymes hydrolyzing
disaccharides into monosaccharides (they are produced
in the intestinal wall) – named disaccharidаses
➢ Sucrase hydrolyses sucrose into glucose and fructose
➢ Lactase hydrolyses lactose into glucose and galactose
➢ Maltase hydrolyses maltose into two glucose molecules
Hyper-glycemia
>200mg/dl
➢ When blood glucose level is higher.
There are physiological and pathological hyperglycemia.
• Physiological hyperglycemia - nutritional and
emotional.
• Pathological hyperglycemia –
pancreatic (diabetes mellitus - deficiency of insulin),
nonpancreatic (increased production of hormones
(except insulin), in some liver diseases, excitation of
central nervous system).
Sometimes, hyperglycemia is not the result of diabetes.
❖ Other medical conditions that can cause
hyperglycemia include:
➢ Pancreatitis (inflammation of the pancreas)
➢ Pancreatic cancer
➢ Hyperthyroidism (overactive thyroid gland)
➢ Cushing's syndrome (elevated blood cortisol level)
➢ Severe stresses on the body, such as heart attack,
stroke, trauma, or severe illnesses, can temporarily
lead to hyperglycemia
➢ Taking certain medications, including prednisone,
estrogens, beta-blockers, glucagon, oral
contraceptives, phenothiazines, and others, can
elevate blood glucose levels.
050. Diagnostic significance of glucose determination in
blood.
The measurement of glucose concentration in blood is
used for diagnostics of diabetes mellitus, steroid
diabetes, Addison disease, some diseases of liver,
functions of endocrine glands.
051. Stage of aerobic oxidation of glucose.
It is the enzymatic breakdown of glucose (C6H12O6) in the
presence of oxygen (O2) to produce cellular energy
(ATP):
C6H12O6 + 6O2 --→6 CO2 + 6H2O + 38 ATP
1. Glycolysis:
• Glycolysis is the anaerobic catabolic reaction of glucose.
• Glycolysis occurs in almost all cells.
• This pathway takes place with or without the presence of
oxygen.
• Aerobic conditions produce pyruvate and anaerobic
conditions produce lactate as the end products of
glycolysis.
• In the eukaryotic cells, glycolysis occurs in the cytosol.
• Glycolysis a process where a molecule of glucose is
converted into two molecules of pyruvic acid.
2. Tricarboxylic Acid (Kreb's) Cycle:
The TCA cycle is an aerobic pathway which takes place in
an intracellular organelle called the mitochondria. It
takes pyruvate, the incomplete
• a ten-step process that occurs in the cytoplasm
• converts each molecule of glucose to two molecules of
pyruvic acid (a 3- carbon molecule)
• an anaerobic process - proceeds whether or not O2 is
present ; O2 is not required
• net yield of 2 ATP per glucose molecule
• net yield of 2 NADH per glucose (NADH is nicotine
adenine dinucleotide, a coenzyme that serves as a
carrier for H+ ions liberated as glucose is oxidized.) The
pyruvic acid diffuses into the inner compartment of the
mitochondrion where a transition reaction occurs that
serves to prepare pyruvic acid for entry into the next
stage of respiration
• consists of a series of enzymes on the inner
mitochondrial membrane
• electrons are released from NADH and from FADH2 and
as they are passed along the series of enzymes, they
give up energy which is used to fuel a process called
chemiosmosis by which H+ ions are actively transported
across the inner mitochondrial membrane into the outer
mitochondrial compartment.
The H+ ions then flow back through special pores in the
membrane, a process that is thought to drive the
process of ATP synthesis.
• net yield of 34 ATP per glucose molecule
• 6 H2O are formed when the electrons unite with O2 * at
the end of electron transport chain.
DNA Replication
The prokaryotic replication process contains several basic
steps, each of which requires certain enzyme activities:
1. DNA uncoiling. As their name implies, the helicases are
ATP-requiring enzymes that catalyze the unwinding of
duplex DNA.
2. Primer synthesis. The formation of short RNA segments
called primers, which are required for the initiation of DNA
replication, is catalyzed by primase.
3. DNA synthesis. The synthesis of a complementary DNA
strand by creating phosphodiester linkages between
nucleotides base paired to a template strand is catalyzed
by large multienzyme complexes referred to as the DNA
polymerases.
DNA polymerase III (pol III), the major DNA-synthesizing
enzyme, is composed of at least ten different subunits.
DNA polymerase I (pol I) is a DNA repaer enzyme. (Pol I is
also believed to play a role in the timely removal of RNA
primer.)
The function of DNA polymerase II (pol II) is not understood.
In addition to a 5'→3' polymerizing activity, all three
enzymes possess a 3'→5' exonuclease activity (An
exonuclesse is an enzyme that removes nucleotides from
an end of a potynucleotide strand.) Pol I also possesses a
5'→3' exonuclease activity.
4. Joining of DNA fragments. Discontinuous DNA synthesis
(described below) requires an enzyme, referred to as a
ligase, that joins the newly synthesized segments.
5. Supercoiling control. The tangling of DNA strands, which
can prevent further unwinding of the double helix, is
prevented by the DNA topoisomerases.
Tangling is a very real possibility, since the double helix
unwinds rapidly (as many as 50 revolutions per second
during bacterial DNA replication).
Topoisomerases are enzymes that alter the linking number of
closed duplex DNA molecules.
The terms "topoisomerase" and "topoisomers" (circular DNA
molecules that differ only in their linking numbers) are
derived from "topology," a form of mathematics that
investigates the properties of geometric structures that do
not change with bending or stretching.
Replication ends when the replication forks collide on the
other side of circular chromosome.
The subsequent separation of the two daughter DNA
molecules is not understood, although a type II
topoisomerase is believed to be involved.
049. The principal and mechanism of transcription.
NECESSARY COMPONENTS
•DNA matrix
•RNA-polymerase
•АТP, GТP, CТP, UТP
•Мg ions
RNA Polymerase
There are 3 RNA-polymerases in eukaryotes (for mRNA,
rRNA, tRNA)
• RNA pol is core of a larger transcription complex
• Complex assembles at one end of a gene (promoter) when
transcription is initiated – transcription initiation
• DNA is continuously unwound as RNA pol catalyzes a
processive elongation of RNA chain
The Chain Elongation Reaction
• Mechanism almost identical to that for DNA polymerase
• Growing RNA chain is base-paired to DNA template strand
• Incoming ribonucleotide triphosphates (RTPs) form correct
H bonds to template
• New phosphodiester bond formed
• Direction 5’-3’
• Speed - 30-85 nucleotides/sec
Transcription Termination
•Only certain regions of DNA are transcribed
•Transcription complexes assemble at promoters and
disassemble at the 3’ end of genes at specific termination
sequences.
050. Modification of RNA. Inhibitors of transcription
(proteins, antibiotics).
During transcription formed 3 types of RNA.
Mrna- messenger rna
• Encodes message from DNA to ribosomes
• Rapidly degraded by nucleases
Trna- transfer rna
• Carries amino acids to translation machinery
• Very stable molecules
Rrna- Ribosomal rna
• Makes up much of the ribosome
• Very stable, majority of cellular RNA
051. Genetic code, properties.
sequence of mononucleotides in mRNA that specifies the
sequence of amino acids in peptide chain
PROPERTIES
1. Unambiguous. In any organism each codon corresponds to
only one amino acid.
2. Code is degenerate. There are multiple codons for most
amino acids.
3. Universal. Codons are the same for all organism.
4. Without punctuation. There are no punctuations between
trinucleotides.
5. Nonoverlapping. Codons do not overlap each other.
052. Codons and anticodons.
CODON – mRNA triplet base sequence responsible for 1
amino acid
ANTIcodon- triplet in trna that can complemtary bind to
codon of mRNA.
053. Ribosomal protein synthesis system, components.
Components
• Codon
• Anticodon (aminoacyl-tRNA)
• Enzymes
• Amino acid
• ATP
1.Activation
• Synthetase catalysis the formation of aminoacyl-1-AMP
• Activating the amino acid through formation of high energy
mixed anhydride bond to form pyrophosphate
2.tRNA linkage
• Specific tRNA binds to actie site of synthetase through an
ester line
• This drives peptide bond formation Amino acid +ATP
>aminoacyl-tRNA +AMP +PP
is the
presence of red blood cells (erythrocytes) in the urine. It
may be idiopathic and/or benign, or it can be a sign that
there is a kidney stone or a tumor in the urinary tract
(kidneys, ureters, urinary bladder, prostate, and urethra),
ranging from trivial to lethal. If white blood cells are found
in addition to red blood cells, then it is a signal of urinary
tract infection.
Causes The most common causes of hematuria[2] are:
• Urinary tract infection with viruses,[2] other sexually
transmitted diseases (particularly in women)[2] or some
bacterial species including strains of EPEC and
Staphylococcus saprophyticus
• Bladder stones
• Kidney stones or ureter stones
• Benign prostatic hyperplasia, in older men, especially those
over 50