Āris Kaksis Riga Stradin's University assistant professor

Chemistry_Research Biochemistry and Bio-Medical Sciences
«The VSEPR Table » Aris Kaksis, RSU “Medical Biochemistry Data Base” © , 2002, >100pp, ≈2.5 MB.
htdocsLoal http://aris.gusc.lv/ChemFiles/ComplexCompounds/PensilvaniaLebanonUniv/PensilvaniaLebanonUniv/VSEPR_table_C0.html
VSEPRtable.html Class work 1. Task for investigation of molecules Word document: Word Macintosh
Molekulu studiju un izpētes praktiskā darba uzdevums Word dokuments: Word Macintosh
3. To investigate the given molecular structures as TGF formated files of compounds using ISISDraw:
carbon(IV)oxide CO2,
carbonate anion CO32-, formic acid HCOOH , methane CH4, amoniak NH3, water H2O,
phosphoric pentachloride PCl5,hexahydroxoaluminate(III) anion [Al(OH)6]3-,
ethene H2C=CH2and ethyne HC tri CH
3. Nosakiet attālumus starp atomiem un valences leņķus TGF formāta molekulāro koordināšu failos ISISDraw :
oglekļa(IV)oksīdam CO2, karbonāta anjonam CO32-, skudrskābei HCOOH , metānam CH4,
amonjakam NH3, ūdenim H2O, fosfora pentahlorīdam PCl5,
heksahidroksoalumināta(III) anjonam [Al(OH)6]3-, etēnam H2C=CH2un etīnam HC tri CH
Valence Electron Shell Pair Formation [7] at p and s bond after hybridization of s valence orbitals has the task
to obtain the working skills with applications RasMol RasWin (RasMol), ISISDraw [2]
(Integrated Scientific Information System for chemical structural molecular studies, investigation and presentation),
which has the goal its employ for chemical studies and investigation of given molecules. Coordination number and
type of the complex compound central atoms structural hybridization. The 3D molecular graphics applied into
Chemscape plugins browser HTML as the plug-in application.

Students can get the knowledge and skills about:
elemental composition and its recognition in the displayed shapes of molecules – wire-frame, stick, stick&ball,
spacefill as well as superimposing the color scheme CPK into symbolic presentation of chemical elements on the
depicted structures of molecules,
bonding geometry (bond – angles, distance, terms of molecular symmetry and antysimmetry)
hybridization types of electron molecular orbitals during bond formation process.

Class work 2. Task for investigation of molecules 1Saccharid14LabA content content 2017
Molekulu studiju un izpētes praktiskā darba uzdevums1Saccharid14LabContLat saturs
«The Saccharide Viewer » Aris Kaksis, RSU “Medical Biochemistry Data Base” © , 2002, >100pp, 21,5 MB
http://aris.gusc.lv/ChemFiles/Saccharides/SSViewer/SSVFrameset.html
«The Saccharide Viewer » [1] attempt 2. has the task to obtain the working skills with RasMol RasWin (RasMol),
ISISDraw [2] applications, which has the goal its employ for chemical structural molecular studies and
investigation of given opened chain and cyclic monosaccharide as well as polysaccharide molecules.
Students can get the knowledge and skills about:
elemental (C, O, H,N, P, S, Na+,Ca2+) composition and its recognition in the displayed shapes of molecules:
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic presentation
of chemical elements on the depicted structures of molecules, haw to convert the given opened chain
mono-saccharides from 3D molecular models into Fisher’s projection. Similar relationships between drawn
Haworth’s projections of pyranose and furanose hemiacetal cyclic structures of mono-, di- and oligo-saccharides
with its presented 3D molecular models.
Optical isomer L or S and D or R recognition using drawn Fisher’s and Haworth’s projections in resemblance
with 3D molecular models.
O-glycoside and N-glycoside links between monosaccharide units on polysaccharide chains.
IUPAC recommendation use for monosaccharide unit designation on polymer chain joined by recommended
nomenclature link description.

Class work 3. Task for investigation of molecules Word document

research
Molekulu studiju un izpētes praktiskā darba uzdevums Word dokuments

pētījums
«The Amino Acid Viewer at pH=7.36» Aris Kaksis, RSU“Medical Biochemistry Data Base”©, 2002,>100pp, ≈2.5MB
htdocsLoal http://aris.gusc.lv/ChemFiles/MCDB108A/tw-amn/aasframes.htm
Drawing the 20 common L-amino [14] acids found in protein as Fisher’s projection at corresponding biological conditions
of water medium pH=7.36 in life systems. That has a task
haw to convert the given molecules from 3D molecular models into Fisher’s projection.
Optical isomer L or S recognition using drawn Fisher’s projections in resemblance with 3D molecular models.
Recognize the 20 amino acids by names, three-letter abbreviation and one letter designation.
Class work 4.
Task for investigation of Glucose Amino Glicans and GlycoProteins Word document:

research
Molekulu studiju un izpētes praktiskā darba uzdevums GlikoProteīnu Word dokuments:

pētījums
«The Protein Glycans Components» Aris Kaksis, RSU “Medical Biochemistry Data Base” © , 2017
http://aris.gusc.lv/ChemFiles/Saccharides/PolySaccharides/HyalurChondroitHeparKeratMucHTM/0GlycoProteinComponents.htm
The constituents of glyco-proteins and proteo glycans [9] has a task to recognize on base of given 3D molecular models
the sequence of given hetero polysaccharides with existing links between units, in order to use IUPAC mono-saccharide
unit abbreviations (for example D-Glucose - Glc) and link designation.
Students can get the knowledge and skills about:
elemental (C, O,H, N, P, S, Na+,Ca2+) composition and its recognition in the displayed shapes of molecules:
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic presentation
of chemical elements on the depicted structures of molecules,
haw to recognize the similarity relationships between drawn Haworth’s projections of pyranose and
furanose hemiacetal cyclic structures of mono-, di- and oligo-saccharides with its presented 3D molecular models.
Optical isomer L or S and D or R recognition using drawn Haworth’s projections in resemblance
with 3D molecular models.
O-glycoside and N-glycoside links between monosaccharide units on polysaccharide chains.
IUPAC recommendation use for monosaccharide unit designation on polymer chain joined by
recommended nomenclature of link description.
Class work 5.
Task for investigation of Immuno Globuline Lysozime Proteins ImmunoGlobulAmed:

research
Molekulu studiju un izpētes praktiskā darba uzdevums lizozīma imunoglobulīna ImmunoGlobulAmedL:

pētījums
«The Immunoglobulin IgG1 Glycoprotein» Aris Kaksis, Eric Martz RSU “Medical Biochemistry Data Base” © , 2017
htdocsLoal http://aris.gusc.lv/ChemFiles/ChimAntibodyMarz/INDEX.htm
The constituent structural features of immunoglobulin IgG1 [11] has a task to recognize on base of given
3D molecular model the two Light chains and two Heavy chains are present in F(ab')2structure.

Blood groups ABO hexa sacharides: http://aris.gusc.lv/ChemFiles/AOBblood-resus/ImmunABO/2frmcont.htm
Students can get the knowledge and skills about:
elemental (C, O,H, N, P, S, Na+,Ca2+) composition and its recognition in the displayed shapes of molecules:
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic presentation
of chemical elements on the depicted 1°, 2°, 3° and 4° structures of molecule IgG1,
what is the complementarity between epitopes and paratopes with its presented 3D molecular models and
N-glycoside links between mono-saccharide units GalNAc on protein Fc units.
Class work 6.
Task for investigation of Myoglobine, Hemoglobine Proteins Word document:

research
Molekulu studiju un izpētes praktiskā darba uzdevums hromo globulīnu Word dokuments

KineMage protein science tools and heme structure using the

ISISDraw
(Integrated Scientific Information System for chemical structural molecular studies, investigation and presentation)
application myoglobin and the human hemoglobin investigation has a task to investigate features and dynamics
for O₂adsorption and desorption from heme Fe2+complex central ion.
The target is to detect coordination number for iron ion Fe2+, into water less heme pocket account related
29 amino acids involved in prevent working of water medium friendly Ox-Red system having high power of oxidation
with well known standard potential Eo= 1.21865 V.
Ox-Red system analyze shows:
O₂ + 4 H₃O++ 4 e- 6 H₂O,
present absent present absent
absent components: they are four 4 hydrogen ions H₃O+and six 6 water H₂O molecules and present components:
they are adsorbed oxygen O₂and electron e-source iron ion Fe2+as complex maker among de-localized electrons
on heme double bond conjugated system.
Students can get the knowledge and skills about:
polypeptide chain sequence order of amino acids beginning from N-terminal first amino acid Val1 which terminates
on C-terminal Gly153 organized as primary 1º polypeptide chain structure.
Secondary 2º structure helices account iron Fe2+position for O₂oxygen adsorption and its alternative replacing
by Histidine His64 nitrogen after O₂desorption. Conformational changes in myoglobine and heme structure
at adsorption – desorption demonstrated by movie oxydeoxy.avi. Composition of human hemoglobin by account and
name these components Relax R and tense T state of hemoglobin O₂oxygen adsorption and O₂alternative desorption.
Di-phospho-glycerate induced O₂desorption via hemoglobin cavity causing conformational change.
Hydrophobic – waterless medium investigation for heme pocket of hemoglobin and evolutionary challenge
of hydrophobic spots on hemoglobin surface in sickle cell anemia having fatal hemoglobin deficiency in north countries
leaving peoples and exposing resistance for peoples against malaria in Africa as well equatorial regions of world too.
Class work 7. a.b.c.
Task for investigation of DNA fragment and tRNA_Tour Word document:

research
Molekulu studiju un izpētes praktiskā darba uzdevums DNS fragmenta un tRNS Word dokuments

pētījums
«The DNA fragment» Eric Martz, Aris Kaksis, RSU “Medical Biochemistry Data Base” © , 2017
htdocsLoal http://aris.gusc.lv/ChemFiles/DnaMarzHTM/INDEX.HTM
«The tRNA_Tour» Aris Kaksis, RSU “Medical Biochemistry Data Base” © , 2017
http://aris.gusc.lv/ChemFiles/CarnegieMellonUChem/Programs/Courses/BiochemMols/tRNA_Tour/tRNA_Tour.html
Task for investigation of DNA binding proteins Histones Word document:

research
Molekulu studiju un izpētes praktiskā darba uzdevums DNS saistošie Histoni Word dokuments:

pētījums
«The NucleoSome Quternary Strucrure» Aris Kaksis, RSU “Medical Biochemistry Data Base” © , 2017
http://aris.gusc.lv/ChemFiles/CLUnucleosome/nucleosome.htm
The mastering DNA fragment in observation has a task obtain the working skills with ISIS Draw applications RasMol

,
RasWin (RasMol) ISISDraw

, which has the goal its employ for chemical studies and investigation of given
DNA and tRNAPhemolecules. Students can get the knowledge and skills about:
elemental (C, O, H,N, P+) composition and its recognition in the displayed shapes of molecules – wire-frame, stick,
stick&ball, spacefill as well as superimposing the color scheme CPK into symbolic presentation of chemical elements
on the depicted structures of molecules,
the essential Watson – Crick base pairing A=T and G tri

C between
adenine = timine and guanine tri

cytosine applied respectively two and three hydrogen bonds per pair.
Hydrogen and hydrophobic bonds supporting primary 1º, secondary 2º, tertiary 3º and quaternary 4º structure
essential stability for single copy of molecule DNA for cell genetic information.
Replication of DNA and drawing the 2D complimentary two strand DNA picture on the student report
using A, U, G and C symbols. Anti-parallelism of DNA strands 5’ and 3’ terminals of strands.
Transcription depicting the 2D complimentary transcript sequences of given DNA as RNA I for first DNA strand
and as RNA II for second DNA strand applying nucleotide symbols A, U, G and C. The Yeast tRNAfeatures:
primary 1º, secondary 2º and tertiary 3º structure and components.
NucleoSomes Quaternaru Structure between the Histone Octamer the DNA binding Proteins and
DNA double helix Supercoile.
Class work 9. Task for investigation of Water structure Word document:

research
Molekulu studiju un izpētes praktiskā darba uzdevums Word dokuments:

pētījums
«Liquid Water Tetramer Strucrure» Aris Kaksis, RSU “Medical Biochemistry Data Base”
© , 2013. http://aris.gusc.lv/ChemFiles/OandH/H2OH2OH2OH2O.html
The mastering Water structure fragment in observation has a task obtain the working skills
with ISIS Draw applications RasMol

, RasWin (RasMol) ISISDraw

and ChemScape MDLi

, ,
which has the goal its employ for chemical studies and investigation of given
water tetramer and water trimer liquid molecules.
Students can get the knowledge and skills about:
elemental (O, H) composition and its recognition in the displayed shapes of molecules :
wire-frame, stick, stick&ball, spacefill as well as superimposing the color scheme CPK
into symbolic presentation of chemical elements on the depicted structures of molecules.