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Biochem 2
photosyn and PPP
| Question | Answer |
|---|---|
| What 2 factors are needed for the light reactions? | ATP and NADPH |
| What 2 things do the light-independent reactions use? And what is accomplished by these reactions? | Uses ATP and NADPH; Fixes CO2 and produces hexoses. |
| Where do the light-independent reactions take place? | in the stroma of plants. (like the cytoplasm of other cells?) |
| What does the calvin cycle do? | It forms hexoses from CO2 and H20. |
| The calvin cycle is the primary ____ fixation pathway. | CO2 |
| How are 3 carbon compounds made into 4, 5, 6, and 7 carbon compounds? | The Calvin cycle. |
| What is 3-phosphoglycerate transformed into? And what is formed? And what is needed in this overall pathway? | Glyceraldehyde 3-phosphate. Hexoses are formed. ATP, NADPH, and the enzyme Rubisco (which is Ribulose 1,5 bisphosphate carboxylase/oxygenase). |
| What is the rate-limiting step in hexose synthesis? (the calvin cycle) | When CO2 is condensed with ribulose 1,5 bisphosphate and produces 2 molecules of 3-phosphoglycerate. |
| What does Rubisco activity depend on? | Magnesium and carbamate (forms a complex that coordinates with CO2 & Rubisco) (lysine is also present too though). |
| When does the body do a wasteful process? And by what enzyme? | Rubisco catalyzes a wasteful oxygenase reaction, (catalytic imperfection). |
| What happens during Rubisco's catalytic imperfection? | Occurs when the carbamate/Mg 2+ complex reacts with O^2 instead of CO^2. (This is a deleterious 'oxygenase' reaction). |
| Where does the ATP and NADPH that is used in the calvin cycle come from? | The light reactions of photosynthesis. |
| What two enzymes are needed to convert some of the products, 'glyceraldehyde 3-phosphate and a hexose, such as fructose-6-phosphate to ribulose 1,5 bisphosphate' | 1. transketolase 2. aldolase These two enzymes help make a 5-carbon sugar from 3- & 6- carbon sugars. |
| Transketolase does what? | Transfers a 2-carbon unit (CO-CH2OH) from a ketose to an aldose. |
| Aldolase does what? | Catalyzes an aldol condensation between Dihydroxyacetone phosphate (DHAP) and an aldehyde (aldose) which forms a ketose. |
| Transketolase makes the 1st reactant smaller and the 2nd one larger b/c it transfers 2 carbons from the first and gives it to the second. | Aldolase does not take any carbons away from the structures but instead combines the two reactants (condenses them). |
| Fructose 6-phosphate; a 6 C ketose, is changed to a 4 C aldose by the enzyme transketolase. (b/c takes 2 carbons away from fructose 6-phosphate). | Glyceraldehyde 3-phosphate is a 3 C molecule that is converted to a 5 C molecule, Xylulose 5-phosphate |
| What are the 3 stages of the light-independent reactions? | 1. Fixation 2. Reduction 3. Regeneration of acceptor |
| What pathway supplies a significant amount of NADPH? | The Pentose Phosphate Pathway (PPP) |
| Where are the 3 places the pentose p. pathway is predominantly found? | -Cytosol of liver -kidney -adrenals |
| What provides a mechanism for being able to use 5-carbon sugars from the diet and to interconvert between 3-, 4-, 5-, and 6-, & 7- carbon sugars? | The Pentose phosphate pathway. |
| Is the direction of the pentose phosphate pathway defined? | No, sugars are only interconverted as determined by the supply. |
| What type are the first 2 steps of the pentose phosphate pathway? | There are 2 oxidative steps at the beginning. |
| What does the enzyme glucose 6-phosphate dehydrogenase do in the pentose phosphate pathway? | It reduces glucose-6 phosphate (an alcohol at the top) to 6-Phosphogluconolactone, an aldehyde by using NADP to grab the 2 H's. (carbonyl group on the top carbon). |
| Which step in which pathway is an irreversible reaction, specific for NADP and highly regulated? | The glucose 6-phosphate dehydrogenase step. |
| What inhibits the glucose 6-phosphate dehydrogenase step? | High NADPH levels and high fatty acyl-CoA levels. (?) |
| What activates the glucose 6-phosphate dehydrogenase step? | Low NADPH levels |
| What does the enzyme 6-Phosphogluconate dehydrogenase catalyze? | It catalyzes a 2-step reaction where a carboxyl group is taken off 6-Phosphogluconate, as well as 2 H's (which then reduces NADP to NaDPH), to a final product of RIBULOSE 5-PHOSPHATE. |
| Which step in the PPP produces CO2 and NADPH? | The 6-Phosphogluconate step, which is catalyzed by 6-Phosphogluconate dehydrogenase and produces Ribulose 5-phosphate. |
| What is Ribulose 5-Phosphate used for? | -To make nucleotide (Nucleotide synthesis) -As a substrate for non-oxidative reactions of the PPP. |
| What is a nonoxidative reaction in the pentose phosphate pathway? | The Isomerization of Ribulose 5-phosphate to Ribose 5-phosphate. |
| Phosphopentose Isomerase does what change? | Phosphopentose Isomerase converts a ketose to an aldose (Ribulose 5-phosphate to Ribose 5-phosphate). (and there is an enediol intermediate). |
| What happens if ribose 5-phosphate (from the PPP) is not needed to make any more nucleotides? | Ribose 5-phosphate is converted to glycolytic intermediates when it is not needed for nucleotide synthesis. |
| What is the rate limiting step of the pentose phosphate pathway? | The glucose 6-phosphate dehydrogenase step where NADPH is made. |
| How is Glucose 6-phosphate partitioned between the pentose phosphate pathway and Glycolysis? | The concentration of NADP levels in the cytoplasm. |
| What controls the oxidative phase of the PPP? | The cytosolic ratio of NADP/NADPH, which ensures that NADPH is not generated unless it is needed. |
| What are the 2 possible pathways that Glucose 6-phosphate can go towards? | Glycolysis or the Pentose Phosphate pathway. |
| Glycerophospholipid synthesis is driven by the energy in the ___________ bonds of _____. | anhydride; CTP (cytisine triphosphate) |
| Glycerophospholipid synthesis can begin from an activated _____________ or activated ____________. | phosphotidate; alcohol. |
| CDP-diacylglycerol reacts with __________ to form a glycerophospholipid. | alcohol. |
| What are the precursors to make sphingolipids? | Palmitic acid and serine. |
| What 2 cmpds make sphingomyelins? | A ceramide and a phosphorylcholine. |
| How are cerebrosides made from ceramide? | By adding a monosaccharide to the C1-OH group of ceramide. (instead of the phosphoryl group being added on). |
| What is the activated precursor in cerebroside synthesis? | UDP-sugars. |
| Cholesterol is made in 5 stages from ______. | Acetyl CoA. |
| What is the 6 carbon molecule made from acetyl-CoA in cholesterol synthesis? | Mevalonate. |
| Cyclization of squalene forms what? And in what process? | The steroid 'lanosterol'; Cholesterol Synthesis. |
| What enzyme is the target of the statins? And what do they try to do? | HMG-CoA reductase. Inhibit the enzyme to stop cholesterol from being produced. |
| Condensation of acetoacetyl-CoA and acetyl-CoA forms _______________________. | 3-hydroxy-3-methylglutaryl CoA (HMG-CoA). |
| What is the structure of acetoacetyl-CoA? | Has 4 carbons, including 2 carbonyl groups, as well as a thiol (S-CoA group). |
| What is the structure of acetyl-CoA? | Has a methyl group on the end of the carbonyl group that is attached to an S-CoA group. |
| What does HMG-CoA stand for? | 3-Hydroxy-3-methylglutaryl CoA |
| Make a notecard with HMG-CoA structure | glutaryl? |
| HMG-CoA can undergo which 2 fates (??) | |
| What general energy reactions does GTP take part in? | GTP drives 2 energy-requiring steps in PROTEIN SYNTHESIS. |
| General function of UTP in reactions? | UTP activates SUGARS during POLYSARCCHARIDE SYNTHESIS |
| General function of CTP in reactions? | CTP activates precursors during PHOSPHOLIPID SYNTHESIS. |
| What are the 4 important roles of nucleotides in biochemistry? | 1. Energy released from breaking anhydride bonds b/w the P of nucleoside triphosphates, drives most energy-requiring rxns in the cell. 2. Nucleotides part of structure of many coenzymes 3. Nucleotides allosterically regulate many enzymes cont. on another |
| What is the 4th role of nucleotides in biochemistry? | Nucleotides are the building blocks of the nucleic acids DNA and RNA. |
| What 3 parts make up a nucleotide? | 1) a ribose of 2' deoxyribose 2) nitrogen base (purine or pyrimidine) attached to the ribose 1' carbon 3) a phosphate group or groups, usually attached to the ribose 5' carbon |
| What is the structure of adenine? The type of base it is? And the ending used w/ it? | -2 fused rings w/ an NH2 group attached to the C6. Purine. -osine. |
| How is counting done with purines? | #1 N begins at 10:30 p.m. (on the 6-membered, left ring) and then count counter-clockwise |
| Structure of guanine? Type of base it is? And the ending used with it? | -2 fused rings w/ a carbonyl group on the 6 C, and an amine grp on C2 of the 6-membered ring. |
| Where are hypoxanthine and xanthine seen? And what kind of bases are they? | As key intermediates in purine nucleotide synthesis and degradation. Are purine bases. |
| Where is thymine found? | Is present in DNA (though rarely tRNA will contain some thymine as well as some uracil). |
| What base is a key intermediate in pyrimidine synthesis? | Orotate (orotic acid). |
| Where is position #1 on pyrimidine ring structures? How is counting done? | N #1 starts at 6:00, and then count counterclockwise. |
| Sugar + base = | Nucleoside |
| The names of purine nucleosides end in? | -osine. |
| The names of pyrimidine nucleosides end in? | -idine. |
| The one that does not follow exact naming rules for nucleosides = hypoxanthine - | Ribose + the base hypoxanthine = nucleoside INOSINE. |
| How does a nucleoside get to become a nucleotide? | By adding one or more phosphates to the sugar part of the molecule. (Usually by an ester linkage to carbon 5' of the sugar) |
| If link 2 acids together (2 phosphates together) what kind of bond is this? | An anhydride bond. (Not all bonds are anhydride bonds, also have phoso-diester bonds in many of these structures. |
| AMP = adenosine monophosphate = adenylate | CMP = cytidine monophosphate = cytidylate |
| dGTP = deoxyguanosine triphosphate | dTTP = deoxythymidine triphosphate (for thymidine nucleotides, the prefix "d" is usually dropped, since ribothymidine is not a major nucleotide |
| Base tautomerization: where are the molecules typically leaning towards? | The keto form. (Remember these structures). (though the reactivity more closely resembles the reactivity of an amide b/c of the adjacent nitrogen). |
| In single-stranded nucleic acids, how are the nucleotides linked together? (give specific carbons) | Nucleotides linked by phosphodiester bonds b/w the 5' ribose carbon of 1 subunit & the 3' ribose C of the preceding subunit. |
| How are double-stranded nucleic acids formed? | By complementary base-pairing of DNA subunits- A&T, A&U, G&C. |
| What enzyme converts ribonucleoside disphosphates to deoxyribonucleoside diphosphates | ribonucleoside reductase |
| Where does most dUMP come from? | From these steps: 1. Reducing CDP 2. Deamination of dCMP to dUMP (enzyme dCMP deaminase is used) |
| What is the basic version of Thymidine synthesis? | 1. Methylation of uracil base of dUMP (catalyzed by thymidylate synthase; and also requires the enzyme dihydrofolate reductase DHFR). |
| What is the main difference between pyrimidine synthesis and purine synthesis? | Purines are synthesized while attached to ribose-phosphate, while pyrimidines can be synthesized as the free base. |
| What is the initial nucleotide formed during pyrimidine synthesis? And what does it get converted into? | OMP (orotidine monophosphate), which then is converted to UTP and CTP via a linear pathway. |
| Except for 1 step, pyrimidine nucleotides are synthesized where? | The cytosol. |
| What is needed for De Novo synthesis of pyrimidine nucleotides? | Bicarbonate, NH3 (directly from NH3 in bacteria, but NH3 from Gln in eukaryotes), 2 ATP; gives carbamoyl phosphate, combine with aspartate to form pyrimidine ring. |
| What are the 6 steps to make UMP? (uracil monophosphate) | 1. Form carbamoyl phosphate (has an NH2 group, carbonyl group, and phosphate group). 2. Synthesis of carbamoyl aspartate 3. Ring closure to form dihydroorotate 4. Oxidation of dihydroorotate 5. Acquisition of ribose phosphate moiety 2. |
| What is the 6th step in the synthesis of UMP? | 6. Decarboxylation of OMP to form UMP |
| How is UMP converted to CTP? |
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