Use these study questions to guide your review of the material. They are not meant to be comprehensive. Topics covered in class, but not covered in the study questions may appear on the exam. Lecture 15: Of catabolism and anabolism, which process produces energy, which process uses energy? Catabolism- produces energy Anabolism- Uses energy Where does most of the energy for biosynthesis come form? Many biosynthetic reactions are endergonic; thus require energy input (derived from exergonic reactions) What molecule is a major source of reducing power (i.e. electrons) for biosynthesis? NADPH What is an amphibolic pathway? A biochemical pathway that serves both anabolic and catabolic processes. An important example of an amphibolic pathway is the Krebs cycle, which involves both the catabolism of carbohydrates and fatty acids and the synthesis of anabolic precursors for amino-acid synthesis (e.g. α-ketogluturate and oxaloacetate). Are all the enzymes in an amphibolic pathway running in the catabolic direction the exact same as those used when the pathway runs in the anabolic direction? Can some of the enzymes be different – i.e. for one step the anabolic direction uses enzyme b while the catabolic direction uses enzyme a? Can all the enzymes be different? Name 3 ways to fix CO2. The main pathway to fix CO2 is the calvin cycle also called Reductive Pentose Phosphate Pathway, Anaplerotic Reactions Reversce TCA cycle ****Does the calvin cycle take place in a soluble compartment of the cell or on membranes? It is a dark reaction?- so it would take place in the chloroplast stroma?? Souble compartment What type of organism fixes carbon via the calvin cycle – autotroph or chemotroph? The fixcation of Carbon takes places in autotrophs What are the 3 stages of the calvin cycle? Carboxylation Reduction Regeneration What is the key enzyme required for the carboxylation stage? RuBP What happens during the reduction stage of the calvin cycle? The use of ATP and NADPH from light is converted to Glyceraldehycde This reduction cycle typically results in G3P and uses ATP and NADPH What are the purposes of the regeneration stage of the calvin cycle? Regeneration of RuBP so that reaction can be continually Produces Carbohydrates Similar to Pentose Phosphate Pathway What pathway is similar to the regeneration part of the calvin cycle? Pentose Phosphate Pathway How many turns of the Calvin cycle, how many CO2’s are required to make glucose (a 6-C sugar)? 5 turns of the calvin cycle, 6 Co2 are needed to make 1 glucose (6c Sugar) What is an anapleurotic reaction? What is its purpose? Anaplerotic Reaction is used by all organisms to FIX SMALL AMOUNTS OF CO2 Occurs via some reactions in TCA cycle hat are reversible What is the reverse TCA cycle? it is when the whole cycle can run in reverse in some anaerobes and archea (prokaryotes that have given rise to eukaryotes and have characteristics that are similar to both eukaryotes and prokaryotes) Incroporates 4 carbons per turn Uses 4-5 atp per turn What is the key protein required for fatty acid biosynthesis? Acetyl Carrier Protein Is the growing fatty acid chain released from ACP (acyl-carrier protein) in between each addition of carbon units during synthesis of a fatty acid?*************** No because that enzyme holds it together… (ACP holds it as it is being synthesized Lecture 16: What is difference between assimilatory nitrogen reduction and dissimilatory nitrogen reduction? Which process is used to get nitrogen for biosynthesis? ews Why do cells need to incorporate nitrogen? If microbes have ammonia (NH4+) and nitrate (NO3) available to use, which will they use first and why? Can plants or other eukaryotes carry out nitrogen N2 fixation? No, because Nitrogen Fixation only happens in Eukaryotes ****What is N2 reduced to as a result of nitrogen fixation?***** Nh3 and Nh4 .. reduced to ammonia What enzyme is required for nitrogen fixation? Nitrogenase enzyme is required for Nitrogen Fixation. What is reductive amination? What is the key enzyme involved? When NH4+ is incorpoprated generated Glutamine, the key enzyme involved is Glutamate Dehydrogenase (GDH) What are transaminases? What molecule do they transfer NH3 from? What are the steps in the glutamine synthetase/glutamate synthase pathway to incorporate NH3 into glutamate? What does each enzyme do? Where do the side chains of amino acids come from? They come from different cycles.. tca cycles.. reductive part of the calvin cycle.. and the pentose phosphate.. Lecture 18-19 What are the differences between nitrogenous base, nucleoside, and nucleotide?Nitrogenous base and sugar are copmpenents of Nucleic Acids called NucleosideNucleoside and Phosphate are called Nucleotide What are the base-pairing rules? A pairs with T (2 H Bonds) and slightly weaker G pairs with C (3 H Bonds) Purines pair with Pyrimidines What bases are purines? pyrimidines? Purines: have 2 rings and an A and G (relatively Big)Pyrimidines: U,T and C have one ring (relatively small) ***How are nucleotides connected in nucleic acids? Between what parts of the nucleotide is this linkage formed? By phosphodiester bonds.. and the linkages between 3 prime hydroxyl and 5 prime phosphates What are the differences between major and minor grooves of DNA? Major Grooves are Wide Minor Grooves are narrow What does it mean that DNA strands are antiparallel? That the two strands run opposite from each otheri. Strand 1 runs 5’-3’ ii. Strand 2 runs 3’-5’ What does it mean that DNA replication is semi-conservative? That one strand of the parent DNA and one strand of new DNA Semiconservative Replication…. Each daughter of the two has one parental thant One strand of old and one strand of new Each parental strand is conserved Two parental strands separate and serve as templates for synthesis of new strands What is the origin of replication? the replication forks? Which moves? Origin of Replication- where Replication is initiated at precise point on chromosome (oric).. this is Static Does not move Replication forks- is where Active DNA replication occurs (these arise from ORIC) this is Dynamic it moves What does it mean that replication is bidirectional? Replication is BIDIRECTIONAL from a single origion: replication forks move in opposite direction from the origin. What are the steps of DNA replication and what role do the following proteins play? DNA polymerase III- DNA Polymerase 3 catalyzes synthesis of new DNA strand both leading and lagging SSB- (single stranded DNA binding proteins) Keeps strands apart but do not cover up the bases DNA gyrase- Relaxes DNA Primase- makes a short RNA primer Helicase- recruits primase Ligase- Seals the Nick RNase H- DNA polymerase I- Fills in the GAP Which of these enzymes is a topoisomerase?******************** >> is basically cuts the DNA DNA gyrase What direction is the DNA template read? New strand synthesized? DNA sequence of the template strand is read 3’ to 5’ RNA chain is Synthesized 5’-3’ just like in DNA replication. What is the difference between lagging strand and leading strand synthesis? Why are they different? Leading Strand synthesis is continous in the direction of the opening replication fork Lagging strand synthesis is discontinuous and moves in the direct opposite of the opening replication fork. Given the following sequence of a DNA strand 5’-AGGCTTAAG-3’, what is the sequence of the complementary strand? Remember to note the polarity, i.e. 5’ and 3’ end. If this sequence were RNA instead of DNA what would the sequence be? What is the difference between a ribonucleic acid and a deoxyribonucleic acid? DNA has Thymine and RNA has Uracil RNA is single stranded, DNA is double stranded. How is DNA compacted so that it can be contained inside bacteria? Bacteria are prokaryotic so they have super coils that Help Compaction of dna What are histones, nucleosomes, and chromatin? Are they found in prokaryotes or eukaryotes? Histones – coil DNA into Nucleosimes (found in Eukaryotes) Nucleosomes- compact together to form chromatin (found in Eukaryotes) Chromatin- Chromatin is the complex combination of DNA and protein that makes up chromosomes. It is found inside the nuclei of eukaryotic cells.