Summary Class notes - Chemie van het leven

Course
- Chemie van het leven
- 2021 - 2022
- Universiteit Leiden (Universiteit Leiden, Leiden)
- Informatica
319 Flashcards & Notes
1 Students
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Summary - Class notes - Chemie van het leven

  • 1612911601 Chapter 2 - Part 1

  • Organisms and their environments are...
    Subject to basic laws of physics and chemistry.

  • Things that happen in real life also happen in the lab. There aren't many differences in chemistry and biology.

    Example
    that organisms and their environments are subject to basic laws of science:

    • Use of formic acid by ants to protect themselves against predators .
    • Formic acid is a simple molecule, but can be very irritating for someones eys.
  • The role of organic chemistry in medicine and biology is very important.
  • What are virtually all medicines/drugs? (such as aspirin, gleevec and lipitor)
    Organics molecules
  • One of the first man made medicine?
    Aspirin
  • What is the drug lipitor good for?
    Effective drug maintaining cholestral
  • What is the drug gleevec good for?
    Very important anti-cancer drug. --> molecule that is designed for a specific target
  • Certain molecules called: enzymes, can also function as targets for medicine development. (example: gleevec)
  • 1612998000 Concept 2.3: Chemical bonding and the formation and fuction of molecules.

  • Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms. Example: sodium chloride. Usually result in binding interactions.
  • What are chemical bonds?
    Interactions that usually result in atoms staying close together. These attractions are held by chemical bonds.

    So bonds are basically the result of two different atoms sharing electrons between them.
  • What is a covalent bond?
    A covalent bond is the sharing of a pair of valence electrons by two atoms
  • In a covalent bond, the shared electrons count as part of each atom's valence shell.
  • What does a molecule consits of?
    A molecule consists of two or more atoms held by covalent bonds.
  • What is a single covalent bond, or single bond? And what is the difference between a single bond and a double bond?
    A single covalent bond is the result of two atoms sharing one pair of valence electrons. The difference between a single bond and a double bond is that a with a double covalent bond, atoms share two pairs of valence electrons.
  • Chemical bonding: How do we represent in their bound form? Hydrogen molecule--> line between hydrogen atoms is the covalent bond(H-H). 

    Hydrogen has only a single valence electron and therefore can share their electrons with another hydrogen atom forming a single covalent bond.
  • How can the form H-H be abbreviated further with a molecular formula?
    Example: H2
  • 1613084400 Chapter 4 - Part 3

  • Stereochemistry of alkenes --> Geometric isomeres around the C=C double bond. --> cis/ trans alkenes. 
    Cis oriëntations = Z geometry, from the German zusammen, meaning 'together'. The extra groups are on the same side. 

    Trans oriëntations = E geometry, from the German entgegen, meaning 'opposite'. The extra groups are on the opposing side.     

    These are different molecules and have different properties etc.
  • 1613170800 Chapter 4 - Advanced Stereochemsitry: Chirality and Enantiomers

  • What makes an object chiral?
    If an object is a non-superimposable mirror image.
  • What do you need to have to get a stereo isomer?
    A tetrahedron centre that has four different groups attached to it.
  • Example: lactic acid --> lactic acid represents a stereo isomer. There are two different forms, the plus form and the minus form. They are non-superimposible and have therefore different chemical properties.
  • What do chiral objects not have?
    A plane of symmetry
  • What is an achiral molecule? And what is the difference between an achiral molecule and a chiral molecule?
    An achiral molecule has a plane of symmetry, so you can make an imaginery cut down the middle, and have the same image. A charical molecule doesn't have a plane of symmetry.
  • What are enantiomers?
    Entiomers are stereo isomers that are non-superimoposable of each other. Like the two lactic acid molecules. The plus and the minus lactic acid molecules are enantiomers of each other. 
  • What are the most biologically active compounds?
    The most biologically active compounds are chiral.
  • When interacting with a living organism, enantiomeric forms of the same compound can elicit varying effects. 

    Example --> plus limonene and minus limonene. Plus limonene is a sent in citrus fruits, the minus limonene is a sent in pine trees.   

    Another example: thalidomide -->   one form is a safe sedative and in the other form it is a tertogen what will misform the foeutus in pregnant women. 

    another example --> chrystal meth and the vicks inhaler. 

    Aother example -->   fluoxetine,   s-fluoxetine is the enantiomer and the other molecule is a mixture of the possible isomers that you can form of fluoxetine.  The mixture is prozac = antidepressant. The steroe chemically pure form it can be used to treat migraine.
  • All the proteins in microorganisms, plants and animals(including us) are constructed from 20 amino acids building blocks. 

    The 20 'proteinogenic' amino acids all have the same configuration.  The s configuration from Phenylalanine. 

    Why nature chose for one configuration over the other is a mystery.
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Wat zijn purines? En wat voor ringstructuur hebben die?
De base adenine en guanine. Die hebben een dubbele cyclische verbinding. Een 5 en een 6 ring.
Wat zijn pyrimidines? En wat voor ringstructuur hebben die?
De base thymine en cytosine. Hebben een 5 c atoom ringstructuur.
Wat voor verschillende stikstof base zijn er?
- Adenine (A)
- Cytocine (C)
- Guanine (G)
- Thymine (T)
Wat zijn nucleotiden?
Monomeren van het DNA molecuul
Waar is DNA opgebouwd?
Nucleotiden
Wat is translatie?
Het omzetten van een RNA molecuul naar aminozuren met behulp van ribosomen.
Wat is transcriptie?
Het process van omschrijven van DNA naar RNA met behulp van rna polymerase.
Wat zijn steroïden?
Onderdeel van de lipiden. Het zijn organische moleculen met een complexe structuur.  Hydrofoob en hebben een soort basis structuur van vier ringen. Aan die ringen kunnen extra groepen ( bijv. hydroxyl, fosfaat) binden en verhogen de oplosbaarheid in water. Voorbeelden = cholesterol en testosteron.
Wat is metabolomics?
Het bestuderen wanneer en in welke cellen metabolieten aanwezig zijn.
Wat is proteomics?
Het bestuderen wanneer en in welke cellen eiwitten aanwezig zijn.