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==Biology class==
 
==Biology class==
  
The biology classes are given at the UvA Science Park.
+
Recommended book: Essential cell biology (3de edition) by Alberts et al..
 +
 
 +
==Keywords Essential Cell Biology==
 +
(sorry about the sloppy layout)
 +
 
 +
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)
  
Recommended book: Essential cell biology (3de edition) by Alberts et al..
+
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
  
Schedule on [[http://rooster.uva.nl rooster.uva.nl]] under course 'Introduction to Systems Biology'
+
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)
 +
5
  
 
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{{Footer Bioinformatics}}
 
{{Footer Bioinformatics}}

Latest revision as of 13:17, 14 May 2018

Biology class

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

Keywords Essential Cell Biology

(sorry about the sloppy layout)

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) 5




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