Chemische reactiviteit en biomoleculen

Chemical Reactivity and Biomolecules

Studiewijzer 2018/2019

Globale inhoud

Knowledge about most important functional groups in Organic and Biomolecues. Basic understanding of  (bio)chemical reactions and their contribution to the functionality of living cells. Knowledge about the central three classes of biomolecules: peptides/proteins, nucleic acids (DNA/RNA) and lipids.

Studiemateriaal

Literatuur

• Organische Chemie: Clayden, Greeves & Warren, ‘Organic Chemistry’, 2nd edition, Oxford University Press. Biochemie: Stryer et al, ‘Biochemistry’ 8th edition (uitgeverij Freeman).

Leerdoelen

Knowledge about most important functional groups in Organic and Biomolecules. Basic understanding of  (bio)chemical reactions and their contribution to the functionality of living cells. Knowledge about the central three classes of biomolecules: peptides/proteins, nucleic acids (DNA/RNA) and lipids.

The student…

1. can name and classify the different types of covalent (polar/apolar) and non-covalent bonds (H-bridge, van der Waals, polar, ionic)
2. recognizes the spatial structure of an organic molecule and can name it.
3. recognizes and name the different functional groups and understand their physical properties.
4. can draw reaction mechanisms and identify a nucleophile and electrophile.
5. recognizes steric effects and their influence on the outcome of reactions.
6. can distinguish electronic effects (inductive / conjugation) and apply their influence to the outcome of reactions.
7. can draw reaction mechanisms of heterolytic and homolytic reactions according to the "curly arrow" principle.
8. recognizes basic and acidic molecules and can arrange them in water in order of strength.
9. can describe the kinetics (speed equations, equilibria) and thermodynamics (free energy, enthalpy and entropy) of organic and biochemical reactions.
10. can define the differences between the terms intermediary and transition state.
11. understands the influence of solvents on the course of reactions.
12. can list the four types of bio-macromolecules and describe what they are made of.
13. can describe the structure of a membrane / lipid bilayer.
14. can describe the structure, nature and function of a sugar (carbohydrate)
15. understands the different forms of transport through a membrane.
16. recognizes the nature (hydrophobic / hydrophilic / charged) of an amino acid and can place amino acids in a protein.
17. can recognize the four levels of protein structures and describe secondary structure elements.
18. using the Michaelis-Menten equation, you can describe the activity of an enzyme, compare different enzymes and recognize types of inhibition.
19. can describe the effect of allosteric regulation.
20. can recognize and describe the structure of nucleic acids.
21. can describe the process of DNA replication, with the associated enzymes and their effect.
22. can describe the process of transcription, with the associated enzymes and their effect.
23. can explain the different steps in the polymerase chain reaction.
24. can explain the process of protein synthesis.

Onderwijsvormen

• Hoorcollege
• Werkcollege

Lectures provide students with the basic knowledge with will be applied to solve questions (before the seminars). Answers to the questions will be presented by students to students in the seminars.

Verdeling leeractiviteiten

Academische vaardigheden

CR&B is linked to the tutoraat (attendance of tutoraat is mandatory). Based on the lecture material, the tutoraat will involve a writing literature report. To be able to write a good literature report you need all kinds of tools that will be discussed one by one in the tutoraat.

Aanwezigheid

Aanwezigheidseisen opleiding (OER-B):

• Van elke student wordt actieve deelname verwacht aan het onderdeel waarvoor hij staat ingeschreven.
• Als een student door overmacht niet aanwezig kan zijn bij een verplicht onderdeel van het onderdeel, dient hij dit zo snel mogelijk schriftelijk te melden bij de betreffende docent. De docent kan, eventueel na overleg met de studieadviseur, besluiten om de student een vervangende opdracht op te leggen.
• Het is niet toegestaan om verplichte onderdelen van een onderdeel te missen als er geen sprake is van overmacht.
• Bij kwalitatief of kwantitatief onvoldoende deelname, kan de examinator de student uitsluiten van verdere deelname aan het onderdeel of een gedeelte daarvan. Voorwaarden voor voldoende deelname worden van te voren vastgelegd in de studiewijzer en/of op BlackBoard.

Aanvullende eisen voor dit vak:

Attendance of lectures and seminars is not mandatory, but highly-advised. Students are expected to act in a self-responsible manner (attendance of tutoraat is mandatory).

Toetsing

The course will involve the following exams:

Midterm exam (Content: Clayden chapters 4 – 8 and Stryer chapters 2, 3, 12 – 14)

Final exam (Content: Clayden chapters 4 – 8, 10, 12, 14 and Stryer chapters 2 – 5, 8 – 14, 28, 29)

Re-sit exam (Content same as final exam)

The Midterm exam is optional and can contribute up to 1.0 bonus points for the final grade. The amount of bonus is your grade in the midterm exam divided by 10 (e.g. an 8 means 0.8 bonus points). IMPORTANTLY: You need at least a grade of 5.5 in the midterm and final exam to qualify for the bonus. Also the bonus will only be applied for the final exam / resit-exam in the same year.

The final grad is composed of the final exam (accounting for 90 %) and the tutoraat (accounting for 10 %). Both parts final exam and tutoraat must be passed (minimum grade 5.5).

Inzage toetsing

Om een inzagemoment aan te vragen, kun je contact opnemen met de coördinator.

Fraude en plagiaat

Dit vak hanteert de algemene 'Fraude- en plagiaatregeling' van de UvA. Hier wordt nauwkeurig op gecontroleerd. Bij verdenking van fraude of plagiaat wordt de examencommissie van de opleiding ingeschakeld. Zie de Fraude- en plagiaatregeling van de UvA: http://student.uva.nl

Contactinformatie

Coördinator

• T.N. Grossmann