Summary of Advanced Biochemistry (2021)
#Disclaimer:
• This is mainly a summary I wrote for myself. There may be some shortcuts which aren’t
obvious at first glance (e.g. AA = amino acid), and I focused mostly on things which weren’t
clear for ME(!).
• Therefore, it would be better to treat this summary as a supplement for live lectures, their
PDFs and notes you took yourself.
• I added more pictures in the latter 2/3rds of the summary.
#Some tips for you:
• Generally: There are some topics the professors love to ask about and NOT all of them can
be found in the lectures!
• Some classic topics:
o N-Glycosylation
o Cholera toxin & AB5-transporters
o Apoptosis
o Important parts of the cell cycle & cancer
▪ Rb, p53 and regulation
o Nuclear transport (rough)
o Mitochondrial transport (more detailed)
o Try to focus on some signaling stuff, too!
▪ They may ask about Receptor-tyrosine kinases (Ras-Raf-MAPK) etc.
o How would you prove that a protein e.g. has a phosphorylation site at a specific
serine (practical knowledge)?
• Some professors allow you to “fail” your 1st try if you aren’t happy with your grade, but not
all of them do!
o Remember though: You only have 2 tries for the ABC exam!
• Look for old exam questions in the Tübingen Biochemistry Forum (FSBC?)! Those are
important.
o Topics not taught in the lectures can be found here.
• Don’t underestimate the exam. The professors can ask you anything involving biochemistry,
even detailed questions in e.g. oxidative phosphorylation.
• Thoroughly learn ALL of your three chosen MoKos ^^ Even if you think one of them is so
boring the professors will never ask about them.
1
,Biochemistry “very cool talk”:
• Moiety
• Protein-DNA complex
• Acceptor/reducer (reducing agent)
• Electropositive
• (electrode potential…)
• Redox reaction
• Interaction
• Nucleophilic/Electrophilic
• Hydrogen bond
• “this leads to a conformational change”
o = “structural rearrangement”
• “works as a molecular glue, sticking two ends of the protein together, thereby forming a
binding cleft”
• Hydrolysis of GTP
• “conformational change into a more relaxed conformation, which no longer harbors the
binding site for…”
• (“can be directly subjected to …”)
• “they are removed prior to the export”
• Threshold
• “are not well characterized”
• “steric interference”
• Works by a “SODDIT mechanism” (some other dude does it)
• A’ = “A prime”
• Superfluous = überflüssig
• Hinge region
• Epistasis: One gene/allele influences the expression of another
List of some important proteins and what they do (not complete!!):
• NFκB: key transcription factor involved in immune response, inflammation, and
tumorigenesis
o IκB: binds NLS and retains NFκB in the cytoplasm, unless degraded by stress signal
▪ IKK phosphorylates IκB
o In cancers, NFκB is predominantly localized in the nucleus as a result of IκB
hyperphosphorylation
• PTEN: phosphatase at the plasma membrane, catalyzes conversion of PIP3 to PIP2
• Nxf1-Nxt1: Heterodimer, responsible for conventional mRNA transport
• 14-3-3 proteins: Bind pSer and pThr
• ACP: Part of the fatty acid synthase, carries intermediates of the fatty acid synthesis in
between the different reactive centers
• (h)AGT: DNA repair enzyme (O6-alkylguanine-DNA alkyltransferase)
• Sulfotransferases: PAPS + R-OH → PAP + R-OSO3-
o PAPS: 3’Phosphoadenosin 5’phosphosulfate
2
, • Sulfatase: Simply hydrolyze the sulfuric esters
• GEF: GTP/GDP exchange factor
o GAP: GTPase-activating protein
o GDI: Guanine-dissociation inhibitors: inhibit dissociation of one guanine nucleotide,
thereby inhibiting the exchange
• SRP (signal recognition particle): helps with transport of ribosome + nascent polypeptide to
ER transporters
• EDEM (ER degradation-enhancing α-mannosidase-like protein): extracts proteins from
CNX/CNR quality control cycle in ER and facilitates binding to ERAD lectins after mannose
has been removed
• Flippase/Floppase/Scramblase: Flipp specific lipids to the outer/inner leaflet of a membrane
• LTPs (lipid transfer protein): Non-vesicular lipid transport to another membrane
• V-Snare: Synaptobrevin, T-Snare: Syntaxin & Snap25
o “Vesicles have a short way to travel in synapses”
• BiP (Hsp70) = chaperone in the ER, works like CNX/CRT.
o One of the driving forces in translation into the ER
Missing right now:
• Stuff to look up:
o Random stuff:
▪ Nobel prices of recent years
▪ CRISPR/Cas
▪ Vitamins
▪ Structure ATP/NADP+/FAD+
▪ #1AA = 110 Da
▪ If cytosolic proteins are directly exported into mitochondria, when does
glycosylation happen?
o Pathways:
▪ Ras-Raf-MAPK, JAK-STAT
▪ Cell cycle
▪ Oxidative phosphorylation
o Techniques:
▪ SPR (Surface plasmon resonance)
▪ SILAC
▪ TIRF microscopy
▪ EPL (expressed protein ligation?)
o Mechanisms
▪ Kinases
▪ Michael addition
▪ Other basic mechanisms?
3
, Summer semester 2020 (First transport, then signaling)
Schwarzer V1: Nuclear Import
• Nucleus: Antonie van Leeuwenhoek, 1719
o Outer membrane, inner membrane
o Heterochromatin, Euchromatin
o Nucleolus, Nucleoplasm
o Nuclear pore
▪ Gateway through the barrier of the nuclear envelope
• Nuclear transport requires:
o Gateway through the nuclear envelope
o NLS: Molecular label that marks cargo for delivery
o Carrier proteins that transport the cargo
o A driving force for translocation
• Nuclear pore complex:
o 120 nm diameter, 70 nm width, 8-fold rotational symmetry
o Consists of: Cytoplasmic filaments, NPC body, Nuclear basket
o #picture
o Assembled from about 30 proteins, = nucleoporins
o Small proteins <40 kDa can pass without transport by diffusion
o 2 models for NPC ‘filter’:
▪ #Sieve-like gel
▪ #Polymer brush
▪ Both models: β-karyopherins bind FG repeat NUPs
• FG repeats: Phenylalanine + Glycine
o Form hydrogels
o F → S mutated: No hydrogels
o Nup50 (Nup2 in yeast): Direct role in nuclear import
▪ Actively displaces NLSs from importin-α
▪ Facilitates disassembly of importin-α:β-cargo complex and importin recycling
▪ Competition with NLS at Binding site I, high affinity binding at Binding site II
▪ picture
• NLS:
o Monopartite: P-KKKRK-V (SV40 large-T antigen)
▪ SV40 large T antigen: Simian Virus 40, oncogenic and DNA-binding protein
regulating viral replication and transforming the host cell (binding to p53 and
pRB)
o Bipartite: KR-PAATKKAGQA-KKKKL (Nucleoplasmin)
▪ Nucleoplasmin: Chaperone located in the nucleolus
o (arginine-rich)
o (Non-basic type)
• β-Karyopherins: Carrier proteins that carry cargos into (importins) or out of (exportins) the
nucleus
o Importins:
4
#Disclaimer:
• This is mainly a summary I wrote for myself. There may be some shortcuts which aren’t
obvious at first glance (e.g. AA = amino acid), and I focused mostly on things which weren’t
clear for ME(!).
• Therefore, it would be better to treat this summary as a supplement for live lectures, their
PDFs and notes you took yourself.
• I added more pictures in the latter 2/3rds of the summary.
#Some tips for you:
• Generally: There are some topics the professors love to ask about and NOT all of them can
be found in the lectures!
• Some classic topics:
o N-Glycosylation
o Cholera toxin & AB5-transporters
o Apoptosis
o Important parts of the cell cycle & cancer
▪ Rb, p53 and regulation
o Nuclear transport (rough)
o Mitochondrial transport (more detailed)
o Try to focus on some signaling stuff, too!
▪ They may ask about Receptor-tyrosine kinases (Ras-Raf-MAPK) etc.
o How would you prove that a protein e.g. has a phosphorylation site at a specific
serine (practical knowledge)?
• Some professors allow you to “fail” your 1st try if you aren’t happy with your grade, but not
all of them do!
o Remember though: You only have 2 tries for the ABC exam!
• Look for old exam questions in the Tübingen Biochemistry Forum (FSBC?)! Those are
important.
o Topics not taught in the lectures can be found here.
• Don’t underestimate the exam. The professors can ask you anything involving biochemistry,
even detailed questions in e.g. oxidative phosphorylation.
• Thoroughly learn ALL of your three chosen MoKos ^^ Even if you think one of them is so
boring the professors will never ask about them.
1
,Biochemistry “very cool talk”:
• Moiety
• Protein-DNA complex
• Acceptor/reducer (reducing agent)
• Electropositive
• (electrode potential…)
• Redox reaction
• Interaction
• Nucleophilic/Electrophilic
• Hydrogen bond
• “this leads to a conformational change”
o = “structural rearrangement”
• “works as a molecular glue, sticking two ends of the protein together, thereby forming a
binding cleft”
• Hydrolysis of GTP
• “conformational change into a more relaxed conformation, which no longer harbors the
binding site for…”
• (“can be directly subjected to …”)
• “they are removed prior to the export”
• Threshold
• “are not well characterized”
• “steric interference”
• Works by a “SODDIT mechanism” (some other dude does it)
• A’ = “A prime”
• Superfluous = überflüssig
• Hinge region
• Epistasis: One gene/allele influences the expression of another
List of some important proteins and what they do (not complete!!):
• NFκB: key transcription factor involved in immune response, inflammation, and
tumorigenesis
o IκB: binds NLS and retains NFκB in the cytoplasm, unless degraded by stress signal
▪ IKK phosphorylates IκB
o In cancers, NFκB is predominantly localized in the nucleus as a result of IκB
hyperphosphorylation
• PTEN: phosphatase at the plasma membrane, catalyzes conversion of PIP3 to PIP2
• Nxf1-Nxt1: Heterodimer, responsible for conventional mRNA transport
• 14-3-3 proteins: Bind pSer and pThr
• ACP: Part of the fatty acid synthase, carries intermediates of the fatty acid synthesis in
between the different reactive centers
• (h)AGT: DNA repair enzyme (O6-alkylguanine-DNA alkyltransferase)
• Sulfotransferases: PAPS + R-OH → PAP + R-OSO3-
o PAPS: 3’Phosphoadenosin 5’phosphosulfate
2
, • Sulfatase: Simply hydrolyze the sulfuric esters
• GEF: GTP/GDP exchange factor
o GAP: GTPase-activating protein
o GDI: Guanine-dissociation inhibitors: inhibit dissociation of one guanine nucleotide,
thereby inhibiting the exchange
• SRP (signal recognition particle): helps with transport of ribosome + nascent polypeptide to
ER transporters
• EDEM (ER degradation-enhancing α-mannosidase-like protein): extracts proteins from
CNX/CNR quality control cycle in ER and facilitates binding to ERAD lectins after mannose
has been removed
• Flippase/Floppase/Scramblase: Flipp specific lipids to the outer/inner leaflet of a membrane
• LTPs (lipid transfer protein): Non-vesicular lipid transport to another membrane
• V-Snare: Synaptobrevin, T-Snare: Syntaxin & Snap25
o “Vesicles have a short way to travel in synapses”
• BiP (Hsp70) = chaperone in the ER, works like CNX/CRT.
o One of the driving forces in translation into the ER
Missing right now:
• Stuff to look up:
o Random stuff:
▪ Nobel prices of recent years
▪ CRISPR/Cas
▪ Vitamins
▪ Structure ATP/NADP+/FAD+
▪ #1AA = 110 Da
▪ If cytosolic proteins are directly exported into mitochondria, when does
glycosylation happen?
o Pathways:
▪ Ras-Raf-MAPK, JAK-STAT
▪ Cell cycle
▪ Oxidative phosphorylation
o Techniques:
▪ SPR (Surface plasmon resonance)
▪ SILAC
▪ TIRF microscopy
▪ EPL (expressed protein ligation?)
o Mechanisms
▪ Kinases
▪ Michael addition
▪ Other basic mechanisms?
3
, Summer semester 2020 (First transport, then signaling)
Schwarzer V1: Nuclear Import
• Nucleus: Antonie van Leeuwenhoek, 1719
o Outer membrane, inner membrane
o Heterochromatin, Euchromatin
o Nucleolus, Nucleoplasm
o Nuclear pore
▪ Gateway through the barrier of the nuclear envelope
• Nuclear transport requires:
o Gateway through the nuclear envelope
o NLS: Molecular label that marks cargo for delivery
o Carrier proteins that transport the cargo
o A driving force for translocation
• Nuclear pore complex:
o 120 nm diameter, 70 nm width, 8-fold rotational symmetry
o Consists of: Cytoplasmic filaments, NPC body, Nuclear basket
o #picture
o Assembled from about 30 proteins, = nucleoporins
o Small proteins <40 kDa can pass without transport by diffusion
o 2 models for NPC ‘filter’:
▪ #Sieve-like gel
▪ #Polymer brush
▪ Both models: β-karyopherins bind FG repeat NUPs
• FG repeats: Phenylalanine + Glycine
o Form hydrogels
o F → S mutated: No hydrogels
o Nup50 (Nup2 in yeast): Direct role in nuclear import
▪ Actively displaces NLSs from importin-α
▪ Facilitates disassembly of importin-α:β-cargo complex and importin recycling
▪ Competition with NLS at Binding site I, high affinity binding at Binding site II
▪ picture
• NLS:
o Monopartite: P-KKKRK-V (SV40 large-T antigen)
▪ SV40 large T antigen: Simian Virus 40, oncogenic and DNA-binding protein
regulating viral replication and transforming the host cell (binding to p53 and
pRB)
o Bipartite: KR-PAATKKAGQA-KKKKL (Nucleoplasmin)
▪ Nucleoplasmin: Chaperone located in the nucleolus
o (arginine-rich)
o (Non-basic type)
• β-Karyopherins: Carrier proteins that carry cargos into (importins) or out of (exportins) the
nucleus
o Importins:
4
