UNIVERSITY OF COLIMA

FACULTY OF CHEMICAL SCIENCES

“ENGLISH REPORT”
PHARMACEUTICAL CHEMIST BIOLOGIST
BIOCHEMISTRY I

TEACHER: DR. Dalia Marcela Sotelo García

Practice 1. Stereochemical models
TEAM MEMBERS:
Ortiz Salgado Marco Antonio
Rolón Pérez Alfonso Xavier
Ordaz Moreno Itzel Alejandra
Flores Hernández Guillermo
Barajas Gutiérrez Naomi Alejandra

GRADE AND GROUP: 4°B

Coquimatlán, Colima Sunday,May 26th,2024

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Abstract

Stereochemical models play a crucial role in scientific education, particularly in chemistry and
biology, by providing a tangible representation of abstract concepts. This hands-on approach
facilitates the understanding of complex molecular structures and interactions, enhancing
students' grasp of fundamental scientific principles.The practice of constructing
stereochemical models using straws and hot glue proved to be an effective tool for visualizing
the three-dimensional structures of cyclohexane and tartaric acid molecules. This activity
allowed students to explore the concept of hybridization, bond angles, and conformational
changes, deepening their understanding of stereochemistry.The comparison of different
conformations of tartaric acid highlighted the influence of spatial arrangement on molecular
properties and reactivity. This hands-on approach provided a concrete understanding of
stereochemical concepts and their implications in organic chemistry and biochemistry.While
the practice demonstrated the effectiveness of stereochemical models, it also presented
challenges, such as precision in cutting and joining straws.

Introduction
Over the years, stereometric models have evolved significantly in terms of accuracy and
complexity. From the early rudimentary stick-and-ball models used by the pioneers of organic
chemistry, to advanced molecular models built with cutting-edge technology such as 3D
printing and virtual reality, the three-dimensional representation of molecules has undergone
a remarkable transformation.
In academia, stereometric models have revolutionized the teaching of chemistry and biology
by providing students with a tangible way to visualize abstract concepts. These models allow
educators to demonstrate molecular geometry, interactions between molecules, and
principles of structure and function in biology, facilitating student learning and
understanding.
In the vast field of biochemistry, understanding biological molecules at the molecular level is
essential to unraveling the fundamental processes of life. Stereochemical models, with their
ability to three-dimensionally represent complex molecular structures, have been useful tools
in this field. This extension delves into the importance of stereochemical models in

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biochemistry, exploring their role in the visualization and manipulation of key molecules, as
well as in drug design and protein engineering.
In the field of scientific research, stereometric models play a fundamental role in
understanding the structure and function of biomolecules. For example, DNA models have
been crucial for studying DNA replication, genetic recombination, and transcription, providing
a physical representation of the double helix and the molecular mechanisms involved.

Furthermore, stereochemical models are indispensable tools in drug design and protein
engineering. Scientists use three-dimensional models to predict how molecules interact with
their biological targets and to design compounds with specific properties, such as therapeutic
activity or selectivity.

In the field of drug design, stereometric models play a crucial role in allowing scientists to
visualize and analyze the interaction between small molecules and their therapeutic targets.
This ability to model molecular interactions is essential in the development of new drugs and
in the optimization of existing therapies.

Enantiomers are isomers with the same molecular formula and identical functional groups,
but with a spatial arrangement of atoms that makes them non-superimposable with each
other, resulting in unique properties and often different biological behaviors.

Chirality manifests itself in molecules that contain chiral centers, also known as asymmetric
carbons. These centers are linked to four different groups, generating two enantiomeric
forms that are non-superimposable mirror images of each other. This property is crucial in
fields such as pharmacology, where small differences in three-dimensional structure can have
a significant impact on the effectiveness and safety of drugs. To represent the chirality and
spatial arrangement of groups in a molecule, different forms of representation are used.
Among them, the wedge and Fisher formulas stand out. The wedge formula offers a three-
dimensional view, where bonds are shown as lines and asymmetric carbon atoms are
highlighted by wedges that indicate their orientation in space.

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On the other hand, Fisher's formula is a planar representation, where carbon atoms are
shown as points, and the groups attached to them are represented by horizontal or vertical
lines, reflecting their relative spatial arrangement.
At the end of the practice, a group discussion session is held, where students have the
opportunity to share their observations and conclusions, as well as emphasizing the
importance of stereochemistry in the understanding of organic chemistry.
Through the manipulation of physical models, we as students develop spatial visualization
skills and gain a deeper understanding of fundamental stereochemical concepts.
Reference
J.M. Berg, J.L Tymoczko and L. Stryer (2003) Biochemistry 5th Edition. Editorial Reverté. S.A.
C.K Mathews, K.E Van Hilda and K.G. Abren (2002) Biochemistry 3rd Edition. Pearson
Education.

Goals
● Build a light and cheap model.
● Exemplify conformers and diastereomers of chiral molecules
● Given the complete structural formula developed for a compound with two chiral
centers represented on paper with projections: Fisher, Newman and easel.
Materials
● Scissors
● Ruler
● Conveyor
● 16 straws
● Colored paper sheets
● Silicone bars/moldable silicone tubes
● White/transparent glue
● Scotch tape
METHOD/PROCEDURE
● Cut the straws to be used to a certain size depending on whether it is carbon, nitrogen
or oxygen.
● Consider hybridization and its angles.

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 ● Build molecular models of at least 6 atoms.
● Make the cyclohexane molecule using straws.
● Join the carbon joints with the silicone gun.
● Draw the wedge shapes of the cyclohexane model.
● Draw the Fisher projection of the model.
● Check if it is superimposable.
● Make the tartaric acid molecule in different conformations and compare.
● Repeat the same process as with cyclohexane.
RESULTS
Simulated molecules and bonds.

Figure 1: Tetravalent carbon Figure 2: Oxygen and hydroxy group

(Methane). (Acetic acid).

Figure 3: Model tetravalent carbons for the construction of structures with straws..

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Figure 4: Cyclohexane model. Figure 5: Tartaric acid model.

Figure 6: Cyclohexane model with Figure 7: Tartaric acid model

straws as a base . made with a straws.

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Tartaric acid models

Figure 8: Fischer projections of the treo (bottom) and erythro (top) models of tartaric acid.

Figure 9: Enantiomers and diastereoisomers of tartaric acid.

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Figure 10: Thireo and erythro models of tartaric acids in wedge model.

Figure 11: R and S carbons of tartaric acid.

● References:
● Berg, J. M., Tymoczko, J. L., & Stryer, L. (2016). Biochemistry (8th ed.). I reversed.
● Devlin, T. M. (2011). Biochemistry with clinical applications (7th ed.). Panamericana
Medical Editorial.

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Conclusion
Stereochemical models are essential in science education, as they facilitate the understanding
of abstract concepts in chemistry and biology in a tangible way. They provide students with
an effective tool to visualize complex molecular structures and biological interactions,
strengthening their understanding of scientific foundations.

In addition to their usefulness in teaching, stereochemical models are also valuable tools in
scientific research and drug design, allowing researchers to explore and better understand
the properties and relationships of molecules.

Discussion
Practice demonstrated the importance of stereochemical models in the teaching and
understanding of organic chemistry and biochemistry. These models provide a visual and
tactile representation of molecules, making it easier to understand abstract concepts and
visualize molecular geometry and biological interactions. Comparing different conformations
of molecules allows you to explore properties and relationships more concretely, thus
strengthening your understanding of organic chemistry. However, during practice, challenges
arose, such as problems with cutting and gluing the straws, as well as discrepancies in the
order when arranging. This gives the importance of careful planning and effective
communication in laboratory activities, as well as the need to adapt and solve problems in
real time.
Questionnaire
1. What object does not have a mirror image?
2. Describe the difference between configuration and conformation.
3. Why is a meso compound not chiral? Give a biochemical example.
4. What other chemical elements can generate chiral centers?
5. Penicillins are a family of antibiotics, what is their general formula? Assign the R or S
configuration to each of the chiral centers of said formula.
6. Define and exemplify in a molecular scheme: plane of symmetry, center of symmetry,
an axis of symmetry

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 7. The hexose family has several chiral centers, what is the number of members that
exists in nature? What is the number of total members that can exist if they are
synthesized?
8. What is a conformational analysis?
Answers
1. An object that does not have a mirror image is called chiral. A common example is a
human hand.
2. Configuration refers to the fixed spatial arrangement of atoms in a molecule, while
conformation refers to the different orientations that a molecule can adopt due to the
rotation of single bonds.
3. A meso compound is not chiral because it has an internal plane of symmetry that
divides the molecule into two halves that are mirror images of each other. A
biochemical example is tartaric acid.
4. Other chemical elements that can generate chiral centers include sulfur, phosphorus,
nitrogen, and silicon.
5. The general formula of penicillins is C9H11N2O4S. The assignment of R or S
configuration depends on the spatial arrangement of atoms in each specific chiral
center of each penicillin.
6. Plane of symmetry: it is an imaginary surface that divides a molecule into two equal
parts, so that if one half is reflected through the plate, an image identical to the other
half is obtained.
Center of symmetry: It is a point within a molecule in which any point located at an
equal and opposite distance through the center will have an equivalent position.
Axis of symmetry: It is an imaginary line around which a molecule can rotate at a
certain angle and retain its original appearance.

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 7. The hexose family has 16 members in nature. If they are synthesized, there could
theoretically be an infinite number of members.
8. Conformational analysis is the study of the different
9. conformations that a molecule can adopt due to the rotation of single bonds. Helps
understand how different conformations affect the properties and behavior of the
molecule.
Annexes

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 References apa
● C.K. Mathews, K.E. Van Holde and K.G. Ahern (2002) Biochemistry. 3rd Edition.
Pearson Education.
● Fundamentals of Biochemistry. Life at the molecular level. 3rd edition. Madrid: Médica
Panamericana, 2010.
● Lehninger. Principles of Biochemistry. 4th ed.Nelson D. and Cox, M. Editorial Omega
(2005) 1 vol.
● Mathews, 2013. Biochemistry. 4th ed. Mexico, D.F.: Pearson.
● Berg, J. M., Tymoczko, J. L., & Stryer, L. (2016). Biochemistry (8th ed.). I reversed.
● Devlin, T. M. (2011). Biochemistry with clinical applications (7th ed.). Panamericana
Medical Editorial.
● J.M. Berg, J.L Tymoczko and L. Stryer (2003) Biochemistry 5th Edition. Editorial
Reverté. S.A.

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