Lecture week 1 (ICB)

Origin of the microscope

Robert Hooke (30X), Antonie van Leeuwenhoek (300X magnification)

different shapes and function

nerve cell - single celled protozoan - snapdragon flower - macrophage - fission yeast

The central dogma

DNA → RNA → mRNA → proteins

What microscope for bacteria

Lightmicroscope

cell shapes

spherical cells, rod-shaped cells, spiral cells

Size of cells, organelles, molecules and atoms

2 micrometer - 2 milimeter, 200 nm - 2 micrometer, 0,2 nm - 20 nm, 0.2 nm

Fluorescence microscopy

A fluorescent molecule (fluorophore) absorbs photons of a specific colour (excitation) and produces photons with a longer wavelength / less energy (emission), fluorophores (dyes) bind to a specifi cellular structure

Electron microscopy

1000x smaller is observed, more details can be seen

Prokayrotes

Limeted cell organizations, circular DNA strand, no nucleus, bacteria

Cyanobacteria

Photosynthetic bacteria, percursors (voorloper) of chloroplasts in plants

Eukaryotic cell

In plants, animals, fungi. They have membrane-enclosed organelles with different chemical processes.

Cytoplasm & cytosol

Cytoplasm is everything in cell except nucleus, cytosol is everything around the organelles

Difference in degree of DNA packaging

Heterochromatin = highly condensed, inactive DNA

Euchromatin = less condensed, more active DNA

Nucleus

larges substructure, genes for r-RNA are here

Endoplasmic reticulum

Rough ER (with ribosomes) & smooth ER, The outer nucleur membrane is continuous with ER membrane. Functions: phopholipid synthesis, protein folding and modification, synthesis of steroid hormones, sequestration of calcium

Ribosome

Responsible for protein synthesis, consist of 2 building blocks: rRNA and proteins

Golgi apparatus

Membrane-enclosed sacs that modify and sort molecules made in the ER. Transport them to other organelles, the plasma membrane and extracellular space

Mitochondria

Spherical or elongated, 2 membranes generate compartments with distinct chemical properties. Responsible for ATP synthases, cellular respiration

Peroxisomes and lysosomes

Inactivate toxins, breaks down macromolecules

Plant cells

Plastids & photosynthesis, cell wall, large vacuole, no lysosomes, many golgi stacks per cell

Chloroplast

carry out photosynthesis, surrounded by 2 membrane and third green thylakoid membrane is highly folded and stacked into grana = layers of membrane (interconnected and surrounded by stroma). Third membrane is green because chlorophyll has this color

Chloroplasts are plastids

Chloroplasts are a member of a larger family of plant organelles, that can interconvert dynamically so they can change in another kind of plastid (plastids)

Reasons why mitochondria and chloroplast are evolved from bacteria in eukaryotic cell

They have 2 membranes, DNA and circular RNA in inner membrane, divide by binary fission (like bacteria), genes of bacterium transfered to nucleus of host

Protein

Polymers from amino acids

This helps folding proteins

Chaperone proteins

Protein structure

Secondary structure: alpha helices, beta sheets

Tertairy structure: motifs / domains / entire peptide chain

quartairy structure: more polypeptides

Hydrophobic forces

Hydrophobic groups clumb together, to stay as less as possible in contact with water. In proteins is this the amino acid side chains, which cluster together.

Non-covalent interactions

Contribute to protein folding, like hydrogen bonds, van der Waals attractions and electrostatic attractions

Disulfide bonds

also called sulphur bridges are covalent bonds within a protein or between protein. Bond between two sulfides, created by oxidation

Ligand

Enzymes (often proteins) selectively bind a substrate = ligand, with many noncovalent bonds.

Function enzyme

Reduce activiation energy of a chemical reaction, but not the position of the equillibrium

Strategies for enzyme-mediated catalysis

Enzyme binds to two substrate molecules and orient them precisely to encourage a reaction to occur between them. Binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charges that favor a reaction. Enzyme strains the bound substrate molecule, forcing it toward a transition state that faovrs a reaction.

Common (de-)activation mechanism

Phosphorylation: Protein Kinases phosphorylate proteins and Protein Phosphatases dephosphorylate proteins. The consequence of phosphorylation can either be activation or de-activation, depending on the enzyme

Membranes

Phospholipids, molecules with a hydrophilic polar head and 2 hydrophobic tails