Biology class

Recommended book: Essential cell biology (3de edition) by Alberts et al..

Keywords Essential Cell Biology

Chapter 1 - Introduction to Cells
- plasma membrane, cytosol
- nucleus/nuclear envelope, ER, lysosome, peroxisome, mitochondria, chloroplasts, golgi, ribosome
- cytoskeleton (actin, microtubules, intermediate filaments)
- chromosomes (separated by microtubules during cell division)
Chapter 2 - Chemical Components of Cells
- Mol / molar concentration (also how to use)
- bonds: covalent, ionic, hydrogen, Van der Waals (hydrophobic)
- acid/bases, pH scale
- building blocks: sugars = polysaccharides, fatty acids = lipids & membranes, amino acids =
- proteins, nucleotides = DNA RNA (nucleic acids)
- glucose (structure)
- condensation-hydrolysis
- fatty acid/phospholipid (basic structure)
- amino acid (basic structure)
- peptide bond
- (deoxy)nucleotides (basic structure)
- guanine, adenine, thymine, cytosine, uracil (and how they pair)
Chapter 3 - Energy, Catalysis and Biosynthesis
- entropy
- carbon cycle
- catabolic/anabolic
- oxidation/reduction (methane/CO 2 /O 2 )
- activation energy (enzymes)
- standard free energy ∆G
- equilibrium constant, Vmax, Km (effect substrate inhibitor)
- activation of bond by phosphorylation
- oxidation/reduction
- main energy carriers (ATP, GTP, NAD(P)H, FADH 2 , acetyl-CoA
Chapter 4 - Protein Structure and Function
- amino acids (polar (neutral, positive, negative) hydrophobic)
- electrostatic interaction, hydrogen bond, hydrophobic (vd Waals)
- Chapter 5 - DNA and Chromosomes
- DNA/RNA (molecular structure)
- 5’ – 3’
- base paring (AT, GC, AU)
- EMSA
- DNA electrophoresis
- DNA footprinting
- 1chromosomes (24 in humans)
- heterochromatin/euchromatin
- mitosis - Interphase/M phase
- mitotic spindle
- telomere/centromere/origin-of-replication
- nucleus/nucleolus (function)
- chromatin/nucleosome/histones (~170 bp, 8 subunits)
- bacteria like E. coli chromosome ~ 4x10 6 bps
- chromatin remodelling complex (ATP)
- histon modifications (expression / silencing)
- epigenetic inheritance
Chapter 6 - DNA Replication, Repair, and Recombination
- DNA replication/template strand
- Ori / replication forks
- synthesis 5’ to 3’/2 or 3 H-bridges (AT vs GC)/pyrophosphate release
- Okazaki fragment (RNA)
- leading strand/lagging strand
- DNA polymerase (proofreading)/DNA ligase (nicks)
- helicase/primase/sliding clamp
- telomerase
- DNA mismatch/excision repair
- strand break repair/ DAN crossover
- mobile elements/transposon/transposase (L1 & Alu)
- horizontal gene transfer
- replicative/non-replicative
- viruses / reverse transcriptase
- retrovirus
Chapter 7 - From DNA to Protein: How Cells Read the Genome
- transcription/translation
- mRNA/tRNA/rRNA/snRNA/sRNA
- gene doses
- RNA polymerase (5’to3’)
- promoter/sigma factor
- start/stop/termination
- -35/-10/+1
- RNA polymerase types I/II/III
- nucleolus
- RNA capping (cap-binding protein)/poly-A tale
- splicing factor/intron/exon
- spliceosome (snRAN)
- TATA box
- small subunit/large subunit
- genetic code (know global principle)
- start/stop codon
- translation N to C (N-terminus, C-terminus)
- polysomes/polyribosomes
Chapter 8 - Control of Gene Expression
- 26 degrees of (protein) regulation
- minor groove/major groove
- transcriptional activator/repressor
- operon
- regulation of lac operon
- enhancer
- mediator
- DNA bending/looping
- combinatorial control
- histon-modifying enzymes
- chromatin remodeling complex
- post-transcriptional control
- riboswitch
- anti-sense RNA (sRNA, miRNA, siRNA)
- RNA interference
- Genetic competence
- Stochastic gene expression (intrinsic noise)
- Bistable/bimodal/heterogenic regulation
Chapter 11 Membrane structure
- lipid bilayer (~ 5 nm)
- hydrophobic/hydrophylic
- phospholipid structure (fatty acid tail, glyercol, phosphate, headgroup)
- cholesterol (sterol)
- glycolipids
- flip-flop (a-symmetry of bilayers), flippases
- cytosol
- saturated/unsaturated fatty acids
- transporters, anchors, receptors, enzymes
- transmembrane, lipid linked, peripheral membrane protein
- amphipathic helix
- liposomes
- detergent
- lateral diffusion
- FRAP
- cell cortex, spectrin, actin,
- lipid rafts
- glycoproteins (carbohydrate)
Chapter 12 - Membrane Transport
- solute, transporter, channel (gated), pore
- passive/active transport
- electrochemical gradient
- membrane potential, delta psi, delta pH
- coupled transport
- uniport, symport, antiport
- glucose-Na + symporter
- gut lumen, epithelium, tight junction, microvilli
- Na + - K + pump
- osmotic balance
- 3aquaporin
- Na + vs H + driven = animal vs plants/fungi/bacteria
- bacteriorhodopsin
- patch clamp
- ion channel triggers
- resting membrane potential ~ 20 – 200 mV
- Nernst equation
- voltage-gated Na+ channels
- action potential
- axon, dendrites, neurotransmitters
- excitatory/inhibitory stimuli
Chapter 13 – How cells obtain energy from food
- catabolism (anabolism)
- central carbon metabolism
- glycolysis (names of key substrates and flow of ATP and NADH have to be known by heart!)
- citric acid cycle (names of key substrates and where GTP, FADH2 and NADH2 is made
- have to be known by heart!)
- Krebs cycle / TCA cycle
- -kinase, -isomerase, -dehydrogenase, -synthase
- fermentation (lactate. ethanol)
- acetyl-coA
- pyruvate dehydrogenase
- lipid catabolism (cycle)
- anabolic precursors
- glycogen
- gluconeogenesis
- allosteric regulation glycogen synthase/phosphorylase
Chapter 14 – Energy generation in mitochondria and chloroplasts
- oxidative phosphorylation
- ATP-synthase, F 1 F 0 ATPase
- chemi-osmotic coupling
- mitochondria: matrix, cristae
- electron transport chain
- NADH dehydrogenase, ubiquinone, cytochrome b-c1 complex, cytochrome c, cytochrome
- oxidase complex
- ~30 ATP from 1 glucose
- porins in outer membrane
- haem, iron-sulfur center/cluster
- bacteriorhodopsin
- chloroplast, thylakoiden (thylakoid membrane), stroma
- homology + difference chloroplasts & mitochondria
- photosystem I & II, chlorophyll, light harvesting complex(antenna complex), reaction centre
- carbon fixation cycle / Calvin cycle
- Rubisco
Chapter 15 - Intracellular Compartments and Transport
- cytosol, nucleus, ER, golgi, mitochondria, lysosome, endosome, chloroplast, peroxisome
- signal sequence (receptor)
- 4transport types: nuclear, over membrane, vesicle
- nuclear transport cycle (nuclear pore, nuclear transport receptor, Ran(GTP))
- transport mitochondria (receptor, translocase, unfolded proteins)
- transport ER (polyribosomes, SRP, translation stalling, signal peptidase)
- trans-membrane proteins (hydrophobic start/stop sequence)
- ER modifications: glycosylation (oligosaccharide protein transferase, dolichol (glucose,
- manose, N-acetylglucosamine)), disulphide bonds (e.g. antibody)
- endocytosis exocytosis
- cis/trans golgi network
- clathrin coated vesicles (cargo receptor, adaptin, clathrin, dynamin), rab-tethering protein, t/v
- snare proteins
- constitute/regulation secretion
- endocytosis, pinocytosis, phagocytosis
- cholesterol transport (LDL, endosome, lysosome)
- nuclease, protease, glycosidase, lipase, phosphatase (pH in lysosome)
- autophagy
Chapter 16 - Cell Communication
- endocrine, paracrine, neuronal, contact-dependent
- 3 different effects acetylcholine
- membrane permeable (cytosolic receptor) / non-permeable (membrane receptor)
- Nitric oxide (NO) effect on smooth muscle relaxation (2 de (signalling) messenger molecule
- cGTP)
- signal transduction cascade
- protein (de)phosphorylation switch, GTP binding/ase switch
- types of surface receptors (ion channel coupled, G-protein coupled, enzyme coupled)
- G-protein (domains, K + -channel, cAMP, adenyl cyclase, PKA (phosphorylation/transcription)
- Inositol phospholipid pathway (Ca 2+ , phospholipase-C, diacylglycerol, inositol triphosphate,
- calmodulin)
- RTK (Ras(GTP), MAP kinases)
- Notch
- bacterial two-component system (histidine kinase – response regulator)
- quorum sensing (Lux system, biofilm)