2012 GENERAL [5 points]

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1 GENERAL [5 points] 2012 Mark all processes that are part of the 'standard dogma of molecular' [ ] DNA replication [ ] transcription [ ] translation [ ] reverse transposition [ ] DNA restriction [ ] DNA ligation Mark all processes that extend the 'standard dogma' of molecular biology [ ] Reverse transcription [ ] Reverse translation [ ] RNA replication [ ] Reverse recombination [1.0 points] Mark all true statements concerning the genetic code. [ ] almost universal amongst all organisms and DNA-containing organelles [ ] is recoded in every new generation [ ] is degenerated, contains more codon combinations than the number amino acids. [ ] is overlapping, codons usually overlap Indicate all the features that support the endosymbiontic origin of chloroplasts and mitochondria: [ ] both are separated by two membranes from the cytoplasm of their host cell [ ] both contain a nucleus [ ] both have to be newly acquired after cell division. [ ] both contain DNA [ ] both contain ribosomes [ ] both contain proteins. [ ] both contain lipids. [ ] both are involved in energy metabolism.

2 DNA STUCTURE AND ORGANIZATION [5 points] [2.5 points] Depicted in the figure below is schematic representation of a eukaryotic chromosome, showing structural organization at different magnification (higher magnification at bottem, lowe magnification at the top). Assign the correct character for each organizational level of the chromosome. [C] 30 nm fiber [A] double stranded DNA [C] beads (nucleosomes) on a string [D] rosette [E] chromatids [1.0 point] Topoisomerases change the 'linking number' of DNA. Mark all true statements concerning topoisomerases. [ ] Class I topoisomerases break one strand of DNA. [ ] Class II topoisomerases break two strands and are also called a gyrases. [ ] Helicases are another class of topoisomerases. [ ] Transposases are another class of topoisomerases. Mark all true statements concerning the modern (non traditional) definition of a gene. [ ] A gene can code for a protein. [ ] A gene can code for a lipid. [ ] A gene can encode a trna. [ ] A gene can encode a rrna. [ ] A gene can code for a telomere. [ ] A gene can encode a nucleosome.

3 DNA METABOLISM [5 points] [1 points] Mark all true statements regarding DNA replication. [ ] DNA replication is semiconservative. [ ] DNA replication is temperature-independent. [ ] both strands of DNA are replicated at the same time. [ ] DNA replication is degenerate. 1 point Mark all true statements regarding Okazaki fragments. [ ] Okazaki fragments are formed on the 'lagging strand'. [ ] Okazaki fragments are formed on the 'leading strand'. [ ] Okazaki fragments are joined by ligases. [ ] Okazaki fragments are synthesized from polynucleotides. Mark all true statements concerning DNA polymerases [ ] Bacteria (like E.coli) contain several types of DNA polymerases [ ] All bacterial DNA polymerases have a 3' 5' exonuclease activity that mediates 'proofreading'. [ ] DNA polymerases require a short piece of complementary RNA to initiate DNA synthesis. [ ] DNA polymerases do not requite magnesium ions. [ ] DNA polymerases utilises AMP, TMP, GMP and CMP as building blocks. [ ] DNA polymerases I is the main polymerase involved in DNA replication. Mark all true statements concerning the recombination of DNA [ ] Recombination of DNA can occur in eukaryotic meiosis between sister chromatids (=chromatids of the same chromosome) [ ] Recombination of DNA can occur in eukaryotic meiosis between homologous chromatids (=chromatids on chromosomes inherited from the 'father' and 'mother') [ ] Recombination of DNA is one of the mechanisms resulting in variable antibodies in mammals. [ ] Recombination of DNA can be mediated by transposable elements. [ ] Recombination of DNA is preventing/limiting molecular evolution.

4 RNA METABOLISM [5 points] Mark all term that refers to the DNA strand that is used as the direct template for mrna synthesis [ ] coding strand [ ] non-coding strand [ ] non template strand [ ] template strand Mark all true statements regarding transcription: [ ] A template consisting of DNA is essential. [ ] The mrna is synthesised in 5' 3' direction. [ ] Transcription occurs in the golgi apparatus. [ ] Transcription termination can be achieved be a terminator consisting of a hairpin structure. [ ] Many RNA polymerases can work together within a single transcription bubble. Mark all true statements regarding RNA polymerases (DNA-dependent RNA polymerases): [ ] In bacteria sigma (σ) factors determine the genes RNA polymerase transcribes. [ ] The sigma factor is not bound to the RNA polymerase during mrna elongation. [ ] RNA polymerase requires a short piece of RNA as template. [ ] The RNA polymerase-sigma (σ) factor complex binds to the promotor region (-35 and -10 region) of a gene. [ ] RNA polymerase utilizes nucleotide diphosphates as substrates [ ] Because RNA polymerase is present in eukaryotes and bacteria, bacterial RNA polymerase(s) is not a target for antibiotics. Mark all true statements relating to the catalytic function of RNAs [ ] All catalytic RNAs can only be used once per reaction. [ ] RNA exhibits catalytic function in Class I and Class II introns. [ ] Spliceosomes contain snrnas that have catalytic function. [ ] Catalytic RNAs can not be associated with proteins.

5 PROTEIN METABOLISM [5 points] Mark all true statements regarding translation [ ] The mrna template is translated in the 5' to 3' direction. [ ] Every mrna can only be translated once. [ ] The N-terminal amino acid of the generated protein is usually a (f)methionine. [ ] trnas and rrnas are translated by a unique set of codons. Mark all true statements regarding ribosomes [ ] The eukaryotic ribosome consists of a 60S and 40S subunit. [ ] The bacterial ribosome consists of a 50S and 30S subunit together forming a 70S ribosome. [ ] The presence of rrna is not essential for the functioning of ribosomes. [ ] Most viruses contain genes that encode 30S and 20S ribosomal subunits. [ ] Ribosomes are located in the nucleus of eukaryotes. [ ] Ribosomes are located in the cytoplasm of bacteria. Ribosomes have functional sites termed 'A','E', and 'P'. Mark all true statements concerning ribosomes functionality. [ ] The 'A' site houses incoming amino acyl trnas during elongation [ ] The formation of the peptide bond requires energy provided by ATP hydrolysis. [ ] The growing polypeptide is transferred from amino acyl trna located in the P-site to the aminoacyl trna located in the 'A' site. [ ] The N-terminal amino acid of the synthesized protein is usually a formyl-methionine [ ] The ribosome can synthesizes proteins from small polypeptide fragments. [ ] Aminoacyl-tRNAs enter the ribosome through the 'E' site and are transferred to the 'A' site during the termination step. Mark all true sentences regarding codons and anticodons: [ ] Codons and anticodons consist of three nucleotides each. [ ] The third base (5' 3') of the codon is in most aminoacyl trnas not bonded as strongly. to the first base (5' 3') of the anticodon as the other codon-anticodon base pairs. [ ] The anticodon is located at the 3' end of every trna. [ ] The anticodons in trnas are encoded by rrna genes.

6 OXIDATATIVE PHOSPHORYLATION PHOTOPHOSPHORYLATION Mark all true statements regarding the chemiosmotic theory. [ ] Electron transport is utilized to form a proton gradient. [ ] A membrane that is permeable to protons (H + can cross freely) is essential. [ ] ATP synthase utilises a transmembrane proton gradient to generate ATP from ADP and inorganic phosphate (P i ). [ ] The chemiosmotic theory explains energy conversion in mitochondria and choroplasts. [ ] The chemiosmotic theory can explain substrate phosphrylation during glycolysis Mark all true statements regarding the ATP synthase (ATPase). [ ] ATP synthase is located within the mitochondrial matrix. [ ] ATP synthase converts rotation energy into a redox potential in the form of NADPH+H. [ ] Mitochondrial and chloroplastic ATP synthase have a common evolutionary origin and function based on the same mechanism. [ ] ATP synthase contains a Cu-heme center that is crucial in donating electrons to oxygen. [ ] ATP synthase is composed of a F 0 (membrane) and F 1 (extra-mebmbranous head) component. [ ] ATP synthase converts a proton gradient (proton motive force) into rotation. Mark all true statements regarding electron transport in mitochondria and photosynthesis. [ ] FeS clusters and cytochromes carry two electrons at a time. [ ] Chloroplasts contain three types of photosystems. (Quinone-type, FeS-type and Cytochrome type). [ ] Quinones (ubiquinone, plastoquinone) can carry two electrons at a time. [ ] Mitochondrial Complex II interfaces directly with the citric acid cycle (Krebs cycle). Mark all true statements regarding mitochondria: [ ] The inside of a mitochondria (matrix) is homologous to the cytoplasm of a bacterium. [ ] Mitochondria only contain proteins that are coded by mitochondrial DNA. [ ] In humans mitochondria are only inherited maternally, (the father's mitochondria are not present in children). [ ] Reactive oxygen species are generated during proton transfer reactions. [ ] The cristae are connected the outer membrane to permit efficient proton transport. [ ] The inner membrane of mitochondria houses the electron transport chains.