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Overview: Der Text bietet eine detaillierte Übersicht über die Biochemie II Prüfung mit Schwerpunkt auf der Fettsäurebiosynthese und Pflanzenbiochemie. Er enthält spezifische Fragen und Antworten zu biochemischen Prozessen wie der Fettsäurebiosynthese im Cytoplasma und der Rolle von Acetyl-CoA Carboxylase. Zusätzlich werden Strategien zur Vermeidung von Photorespiration bei Pflanzen erläutert. Diese Informationen könnten für Studierende, die sich auf Prüfungen vorbereiten, oder für Fachleute, die ihr Wissen auffrischen möchten, sehr wertvoll sein.
Biochemie II Prüfungsfragen: Fettstoffwechsel und Pflanzenbiochemie
Prüfungsfragen Biochemie II
29.02.2008 06.03.2009 08.01.2010
Fatty acid biosynthesis
1. Which of the following statements concerning fatty acid biosynthesis are correct? If incorrect, give the correct answer! (2 points each)
Wrong, it uses Malonyl CoA
Wrong, fatty acid Biosynthesis occurs in the Cytoplasm; β-Oxidation occurs in the Mitochondira
Wrong, Biosynthesis of fatty acids uses NADPH; β-Oxidation uses NADH
Wrong, it’s a C16 fatty acid (Palmitate); longer ones are made by elongases
Right, it’s regulated by allosteric and Hormonal mechanisms
2. Formulate the initial step of fatty acid biosynthesis (5 points); describe the role of the coenzyme involved (3 points) and explain the thermodynamic rationale behind this reaction step! (2 points)
The first step of the fatty acid biosynthesis is the Biotin-dependent carboxylation of acetyl-CoA to Malonyl CoA.
3. Formulate the initial step in fatty acid biosynthesis! Which enzyme catalyzes this reaction (name!) and which cofactor does it use (5 marks)? Provide a chemical rational for this reaction in view of the thermodynamic constraints of the biosynthesis (5 marks)!
Initial step: look at number 2
Biotinyl-Enzyme catalyses this reaction
It uses Acetyl CoA
Plant biochemistry
1. Photorespiration: Formulate the corresponding reaction with oxygen instead of carbon dioxide (5 points) and explain why this process is called photorespiration (5 points)
It is called photorespiration, because it undoes some work of the photosynthesis; hence it lowers net photorespiration
2. Plant physiology: Describe two strategies of how plants avoid or minimize photorespiration and formulate the pertinent biochemical reactions (5 points each).
1st way: Trap CO2 in form of Oxaloacetate and malate (C4 Metabolism)
2nd way: CAM (Crassulacean Acid Metabolism) plants
3. A team of scientists selects plants for a greenhouse on Mars. The carbon dioxide concentration in the green house is maintained at 10000 ppm. What kind of plants will they choose and why? Explain! (5 marks each)
They would choose C4 plants. They lose less water when they fix carbon and they are able to fix more carbon.
4. Photosynthesis: Chloroplasts are illuminated until the levels of the Calvin-cycle intermediates reach a steady-state. The light is then turned off. How do the levels of ribulose bisphosphate and 3-phosphoglyceraldehyde vary after this point (5 marks each)?
RBP is going to be consumed and transformed into 3PG. RPG can’t be regenerated, because ATP and NADPH is needed.
Nevertheless, CO2 is present, which is used to turn RBP into 2 3PG.
5. Formulate the reaction that leads to fixation of carbon dioxide in C3 plants; give the name and structure of the carbohydrate that is used for this reaction (10 points)
CO2 + RuBP 2 3PG
Ribulose-1,5-bisphosphate
6. Photorespiration: Formulate the corresponding reaction with oxygen instead of carbon dioxide (see above, 5 points) and explain why this process is called photorespiration (5 points)
Amino acid biosynthesis
1. The reaction of pyruvate and alpha-ketobutyrate with hydroxyethyl-thiamine pyrophosphate (TPP) yields alpha-acetolactate and alpha-aceto-alphahydroxybutyrate, respectively. Formulate the analogous reaction with beta-keto-butyrate. (10 points, asked two times)
2. Several neurotransmitters are synthesized from amino acids. Formulate the generation of serotonine, histamine and gamma-aminobutyrate from the appropriate amino acid (2 marks each). Which chemical reaction is always involved in the formation of biogenic amines and what is the name and structure of the cofactor involved (4 marks, asked 3 times)?
Figure 1 Histamine synthese aus Histidin
Figure 2 Gamma Amino butyrat Synthese
A decarboxylase is involved in all processes.
Name of the involved Cofactor is Pyridoxalphosphat.
Structure:
RNA
RNA-processing: Explain the terms intron and exon (4 points) and formulate the reactions that lead to the removal of introns in a hypothetic self-splicing pre-mRNA (6 points) (asked two times).
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Introns are parts of the DNA which are removed after RNA splicing during maturation.
The joined parts in the final RNA hence are made of exons which are joined together.
Purine and Pyrimidine
5.1 Purine metabolism: Formulate the reactions of the purine salvage pathway, give the names of the enzymes involved. Which human disease is connected to deficiencies in purine salvage pathway? Which enzyme is affected in this disease?
Adenine + PRPP (5-phosphoribosyl-α-pyrophosphate) -[adenine phosphoribosyl transferase APRT]-> AMP + PPi
Hypoxanthine + PRPP -[Hypoxanthine-guanine phosphoribosyl transferase HGPRT]-> inosine monophosphate (IMP) + PPi
+-->+
Guanine + PRPP -[HGPRT]-> GMP + PPi
+-->+
Lesch-Nyhan syndrome, causes excessive uric acid production and highly aggressive and destructive behavior (self-mutilation); caused by point mutations in HGPRT
5.2 Pyrimidine biosynthesis: Formulate the reactions required to synthesize carbamoylphosphate, the first step in pyrimidine biosynthesis catalyzed by carbamoylphosphate synthetase II.
HCO3- + glutamine + 2 ATP --> carbamoyl phosphate + glutamate + 2 ADP + Pi
HCO3- ++ 2 ATP -->++ 2 ADP + Pi
6. Transcription
6.1 A novel antibiotic inhibits the de-novo biosynthesis of proteins. Which of the following processes could be affected by the antibiotic? Give a brief explanation.
DNA-replication: would inhibit proliferation but proteins could still be synthesized
Promotor clearance of the preinitiation complex (PIC): does not occur in bacteria, only in eukaryotes
mRNA binding to the large (50S) ribosomal subunit: crucial step to form 70S initiation complex in prokaryotes to start translation
Loading of amino acids to the acceptor stem of tRNA: AA must be bound to tRNA for ribosomes to form polypeptides
6.2 Explain the functional role of transcription factors (TFs) and the formation of the preinitiation complex (PIC)
TFs recognize promotor regions on the eukaryotic DNA, some are required to initiate transcription, therefore essential for synthesis of all mRNAs
Formation of PIC: (TBP=TATA box binding protein; TAF=TBP-associated factors; GTF=general TF)
TFIID (TBP + TAFs) bind to TATA box
TFIIA and TFIIB bind next
TFIIE and TFIIH complete the assembly of the PIC
ATP-hydrolysis powers the helicase activity of TFIIH resulting in open complex formation and transcription start
TFIID remains bound to the TATA box after promotor clearance of the RNA polymerase II
All GTFs but TFIIF dissociate from the transcription “machinery”
7.1 DNA Replication: Which of the following sets of proteins are needed for lagging strand biosynthesis in DNA-replication of linear chromosomes? Briefly describe the role of the proteins that are not involved in DNA-replication. For the correct set provide a BRIEF description of the role of the protein in lagging strand biosynthesis. Which of these five proteins are also required for leading strand biosynthesis in DNA-replication?
Amino acyl-tRNA synthetase: attaches a specific amino acid to the acceptor stem of the belonging tRNA
Elongation factor: required during translation for polypeptide chain elongation
Release factor: used in translation, recognize termination codons, stop chain elongation
Termination factor rho: used in RNA biosynthesis termination in bacteria, enhances the efficiency of spontaneously occurring terminations and induces the termination of non-spontaneous processes
Proteins required in lagging strand biosynthesis:
Primosome: mediates RNA primer synthesis
SSBs: keeping the DNA strands from re-annealing
DNA-ligase: seals nicks by forming phosphodiester bonds after RNA primer has been replaced by dNTPs
DNA-polymerase: DNA-polymerization, proofreading (3’ to 5’ exonuclease activity), removing RNA primer of Okazaki fragment in the lagging strand (recognizes nick, 5’ to 3’ exonuclease activity)
Telomerase (not in correct set of proteins): possesses a short RNA sequence as a template for the extension of the 3’-end of each DNA strand
Also needed in leading strand biosynthesis: DNA-polymerase, SSBs, maybe Primosome (?)
7.2 DNA replication is a semi(dis)continuous process. Describe briefly the differences between leading and lagging strand biosynthesis. This description should explain the role of DNA-polymerase, the primosome, DNA-ligase, Okazaki fragments and RNA primers.
It can only synthesis the new strand from 5’ to 3’ direction. Since replication occurs simultaneously at both strands of a replication fork, one strand is synthesized continuously (in one piece) from 5’ to 3’ (leading strand), and the other strand discontinuously from 3’ to 5’ (lagging strand), meaning small fragments (so called Okazaki fragments) are synthesized and then connected.
Pol I can’t start replication on an “empty” strand, it needs short RNA primers to start.
These primers are synthesized by the primosome, an enzyme assembly consisting of an helicase (separating two annealed bases) and a primase (generates RNA pimer). On the leading strand only one primer is required, on the lagging strand each Okazaki fragment requires a new primer.
Pol I also has a 3’ to 5’-exonulcease activity (proofreading: can cleave bond if wrong nucleotide was inserted) and a 5’ to 3’-exonulcease activity (recognizes a nick, hydrolytically cleaves the strand about 10 bases towards the 3’-end and fills up the gap with dNTPs; this process leaves a nick)
DNA-ligase seals nicks after RNA-primer was removed.
Cytosine gets deaminated to uracil and adenine to the guanine-like hypoxanthine, resulting in AT to GC and GC to AT transitions.
8. Translation: factors/proteins required for generating the bacterial/prokaryotic 70S initiation complex
Required:
NOT required:
GDP
Elongation factor EF-Tu (EF-T, EFs in general) - used for polypeptide chain enlongation
Release factors RF-1, 2 - when bound they initiate transfer of polypeptide to water, recognize termination codons
RF-3 - binds GTP and enhances binging of RF-1 and 2
9.1 Heme-biosynthesis: Formulate the first step of heme-biosynthesis (ALA-synthase reaction) using the initial PLP-bound structure below
Gylcin + succinyl-CoA --> delta-aminolevulinic acid (ALA) + CO2 + HSCoA
9.2 Protein biosynthesis: Describe the importance of substrate specificity of aminoacyl-tRNA synthetase (aaRS) for the process of translation and explain the term identity element in this context
If an amino acid gets attached to a tRNA with the wrong anti-codon, mutations are introduced to protein
Identity elements: bases at the acceptor stem and anti-codon-loop, which are used by the aaRSs to connect the right AA to the right tRNA
How many molecules of acetyl-CoA are required to synthesize palmitic acid? 4P
8 molecules, palmitic acid has 16 C and 2 C‘s are delivered per Acetyl CoA
Biotinyl-Enzyme Acetyl CoA is required.
Which (reduced) cofactor/coenzyme is used in fatty acid biosynthesis?
NADPH NADP+
Formulate the first two reactions from acetyl-CoA to hydroxymethylglutary-CoA (HMG-CoA)? 4P
What is the name of the pathqway leading to phenylalanine, tyrosine and tryptophan?
Shikimate Pathway
Provide the names and structures of two “isoprene” units used in terpene/steroid synthesis. 4P
Squalene und Cholesterol
Define the terms monoterpene, sesquiterpene, di- and triterpene. 4P
Monoterpene=2Isoprene units
Sesquiterpen=3Isoprene units
D…
Which vitamins are synthesized through the mevalonate pathway? 4P
Vitamin K und E
What are porphyrias? 4P
Which building blocks are used for ceramide biosynthesis (2P)? Formulate the initial (PLP-dependent) reaction. 2P
Which central reaction typically initiates the generation of biogenic (active) amines (2P)? Which cofactor is needed for this reaction (2P)?
Which active amines belong to the family of catechol amines 4P?
Give the name of four amino acids used for alkaloid biosynthesis 4P?
Lysine, ornithine, aspartate, tryptophan
Explain the role of adenine phosphribosyltransferase (APRT) and hypoxanthine-guanine phosphoribosyl-transferase (HGPRT) for purine metabolism 4P.
-briefly describe the chemical reactions occurring during the splicing reaction (scheme!) (lasso).
DE
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