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Biochem and Genetics
For Biochemistry and Genetics Fall 2020
| Term | Definition |
|---|---|
| Protein | Macromolecule made of 1 or more polypeptide chains |
| T/F: Animal proteins are much more digestible than plant proteins. | True |
| Amino Acid Structure | Hydrogen atom, carboxyl group, amino group, R group |
| Amino acid most often found in humans? | L amine |
| Amino acid that is protection for bacteria? | D alanine |
| Aliphatic AAs contain? | Hydrocarbon chains |
| Aromatic AAs contain? | Ring structures |
| Examples of aliphatic AAs | leucine, alanine, valine, isoleucine |
| Examples of aromatic AAs | tyrosine, phenylalanine, tryptophan |
| ______ AAs absorb UV light | Aromatic |
| Beer Lambert Law | A=Elc; A-absorption, E-absorption coefficient, l-path length, c-concentration |
| Examples of acidic amines | aspartic acid (aspartate), glutamic acid (glutamate) |
| Examples of basic AAs | lysine, arginine, histidine |
| Describe polar side chains | -Have slight negative charge -Hydrophilic |
| Examples of polar side chains | Serine, threonine, gysteine, tyrosine, asparagine, glutamine |
| Sulfurous AAs | Cysteine, methionine |
| Describe Proline AAs | Side group is bound to amide group and alpha-carbon |
| Amino acids are _____ molecules | amphoteric. (water can act as both a base and an acid) |
| Henderson Hasselbach Equation | pH = pKa + log([A-]/[HA]). |
| All amino acids have at least __ ionizable groups | 2 |
| At pI, which is 100% deprotonated? Which is 100% protonated still? | acid group is deprotonated. Amino group is protonated. |
| Primary protein structure | Amino acid residues in peptide chain |
| Secondary protein structure | Hydrogen bonds between amino acids hold together in sheets. |
| Typical alpha-helix chain is about __ amino acids long. | 11 |
| R-group stick ___ out of the sheet | up |
| Tertiary protein structure | Functional groups interact |
| Types of crystallins | Alpha, beta, and gamma |
| Which maintain elongated fiber shape and lens structure in the eye? | Crystallins |
| What affects light refraction that passes through the lens? | Crystallins |
| What are known as "molecular chaperones"? | Crystallins |
| How do crystallins play a role in cataracts? | Insoluble proteins build with age |
| What is a cone pigment protein? | Rhodopsin |
| 80-90% of the bulk of the eye is _______ | Collagen |
| Collagen builds the ______ for basement membranes | scaffolding |
| Collagen makes up the ________ point for cells. | Anchoring |
| What makes the semiliquid gel of the vitreous? | Collagen |
| Structure of collagen | Triple helix; the 3 peptides are highly hydroxylated |
| There are ___ types of collagen, ___ of which are found in the eye | 29 types; 12 found in eye |
| Type I Collagen | Forms sheets |
| Type V Collagen | Limits Type I diameters |
| Type VI Collagen | Stabilizing molecules for proteoglycans and keratocytes |
| Type II Collagen | Vitreous involvement - vitrosin |
| Type IX Collagen | Links Type II to proteoglycans |
| Type V-XI hybrid Collagen | Controls Type II diameter |
| Type IV Collagen | Forms a spider web for basement membranes |
| Type VIII Collagen | Forms a box spring arrangement for Descemet's Membrane |
| Type VII Collagen | Helps link cells of epithelial tissue and Bowman's |
| Enzymatically catalyzed reactions occur under relatively ______ conditions. | Mild |
| _______ rarely have side products. | Enzymes |
| T/F: We do not reuse enzymes. | False |
| Oxidoreductases | Transfer of hydrogen and oxygen atoms or electrons from one substrate to another. Ex dehydrogenases and oxidases |
| Transferases | Transfer of a specific group (a phosphate or methyl etc) from one substrate to another. Ex transaminases and kinases |
| Hydrolases | Hydrolysis of a substrate. Ex estrases and digestive enzymes |
| Isomerases | Change of the molecular form of the substrate. Ex phospho hexo isomerase and fumarase |
| Lyases | Nonhydrolytic removal of a group of additional of a group of a substrate. Ex decarboxylases, aldolases |
| Ligases (Synthetases) | Joining of two molecules by the formation of new bonds. Ex citric acid synthetase |
| T/F: Each enzyme possesses a unique active site | True |
| Most enzymes have both ______ specificity and ________ specificity | Reaction; substrate |
| Substrate binding models | 1) Lock-and-key model 2) Induced-fit model Perfect fit AFTER binding 3) Allosteric activator Cause a shape change of the active site 4) Allosteric inhibitor Causes shape change back to norm so enzyme stops |
| Define cofactor | Non-protein compounds that activate an enzyme |
| Define isoenzymes | Enzymes that conduct the same reaction but possess slightly different properties |
| Factors affecting enzymes | Temperature, pH, Ionic strength, cofactor availability, and substrate availability |
| Are additional protein subunits cofactors? | Nope |
| Define enzyme kinetics | The study of enzymatic reaction rates |
| Three steps of enzymatic reactions | Enzyme binds to substrate, substrate is converted to product, and product is released from enzyme |
| Smaller Km = ____ affinity | Greater |
| In Lineweaver-Burk Plots, what do the variables mean? | Y axis = 1/v; X axis = 1/[S]; M = Km/vMax; B = 1/vMax |
| Types of Reversible Enzymatic Inhibitors | Competitive (does not allow substrate to bind), Non-Competitive (does not allow substrate to bind), Uncompetitive (Binds to allosteric site and prevents conversion of substrate to product), |
| What causes change in kM only? | Competitive Inhibitor |
| What causes change in vMax only? | Non-Competitive Inhibitor |
| What causes change in kM and vMax? | Uncompetitive Inhibitor |
| What is a tear film enzyme? | Lysozyme |
| Sodium-potassium ATPases | Sodium-potassium pump powered by ATP. Important in corneal hydration and intraocular pressure (aqueous fluid generation) |
| What can failure of Na-K pump cause? | Stromal edema, subepithelial fibrosis, epithelial bullae, corneal guttata |
| Lactate Dehydrogenase (LDH) | Used in the production of ATP during anerobic conditions by converting pyruvate to lactate |
| LDH1 is present in? | Heart, RBC |
| LDH2 is present in? | Heart, RBC |
| LDH3 is present in? | Lungs and spleen |
| LDH4 is present in? | Lungs and spleen |
| LDH5 is present in? | Skeletal muscle, liver |
| Most LDH is used in ________ conditions | Anaerobic |
| Which LDH is in the retinal photoreceptors? | LDHk. Similar to LDH5 but phosphate is on tyrosine 238 and it is bound to other proteins. |
| Warburg effect | High lactate couple with high glucose and oxygen consumptions |
| Retina is a very _______ environment | aerobic |
| Aldos Reductase | Found in the seminal vesicles and liver. Also in lens, retina, Schwann cells, RBCs |
| Structure of vitamins | Individual units (not linked together or polymers) |
| Is energy yielded by vitamins? | No. They assist other enzymes. |
| Water-soluble vitamins move where? | Directly into the blood |
| Fat-soluble vitamins move where? | They enter lymph and then blood. They must use things like bile to fully absorb them and use them. |
| Consumption frequency of vitamins | Fat soluble vitamins are stored more than water-soluble ones. Water soluble ones must be eaten more regularly. |
| What are the water-soluble vitamins? | Thiamine (B1), Riboflavin (B2), Niacin (B3), Pantothenic Acid (B5), Pyridoxine (B6), Biotin (B7), Folate (B9), Colbalamin (B12), Vitamin C |
| What are the fat-soluble vitamins? | Vitamin A, Vitamin D, Vitamin E, Vitamin K |
| Thiamine Functions | B1! Part of coenzyme thiamine pyrophosphate. Helps in transferase and carboxylase reactions. |
| Thiamine Deficiency | Wernicke-Korsakoff Syndrome. Trouble standing, slurred speech, stumbling around. Also Beriberi. Dry form affects nervous system and wet form affects cardiovascular system. |
| Riboflavin Function | B2! Serves as coenzyme in energy metabolism. Flavin mononucleotide, flavin adenine dinucleotide |
| Riboflavin Deficiency | Rare. Angular cheilitis (oral), photophobia (ocular), scrotal dermatitis (genital). UV and radiation destroy riboflavin |
| Niacin Functions | B3! Has two structures, nicotinic acid and nicotinamide, which is the major form of niacin in blood. The body manufactures this from tryptophan. Only occurs after protein synthesis needs have been met, though. |
| Niacin Deficiency | Pellagra. Diarrhea, dermatitis, dementia. Can cause death. Also Hartnup's Disease is a kidney condition that can cause niacin deficiency. |
| Niacin Toxicity | Via supplementation in pill form. Niacin flush - itching and tingling, can be painful to the point where it immobilizes you. You become flushed dark red. |
| The absorption of which vitamin is affected by alcohol consumption? | B1, thiamine |
| Which of the following vitamins is affected by alcohol consumption? | B1 and B3, considering B1 is used as a cofactor in the conversion of tryptophan into B3. |
| Pyridoxine Functions | B6! Shows up in three forms. Pyridoxal, pyridoxine, and pyridoxamine. Conversion to coenzyme PLP. Helps in glycogen metabolism. Also helps in conversion of tryptophan to niacin or serotonin. Helps with synthesis of heme, nucleic acids, and lipids. |
| Pyridoxine Deficiency | Rare. High protein intake requires more pyroxidine. Can cause depression, irritability, and confusion. Alcohol and isoniazid (TB med) will also cause this deficiency. |
| Pyridoxine Toxicity | Only happens through supplementation. Irreversible nerve degeneration. Destruction of dorsal root ganglia. |
| Biotin Functions | B7! Coenzyme that carries activates carbon dioxide. Critical in TCA cycle. Participates in gluconeogenesis and fatty acid synthesis. Also in synthesis of isoleucine and valine. |
| Biotin Deficiency | Rare. Hair loss. Can get this from eating 2 raw egg whites daily for several months. GI bacteria produce biotin naturally. |
| Folate Functions | B9! Known as folic acid! Active forms include dihydrofolate and tetrahydrofolate. Transfers single-carbon compounds during metabolism. Converts B12 to active enzyme form. Helps with DNA synthesis and repair. Aids in rapid cell division and growth. |
| Folate Deficiency | Neural tube defects (spinal bifida). Folate has been added into grain products. Folate can mask a B12 deficiency. |
| Colbalamin Functions | B12! Depends on folate for activation to an extent. Helps with rengeneration of methionine, synthesis of fatty acids, synthesis of DNA, and synthesis of RNA. In digestion and absorption, stomach hydrochloric acid releases B12 from proteins. |
| Colbalamin Deficiency | Inadequate absorption. Vegan diets. Excessive alcohol intake. Tape worms. |
| Vitamin C Functions | Cofactor in collagen formation. Matrix for bone and tooth formation. Helps convert tryptophan to serotonin. Antioxidant. Helps deactivate histamine. |
| Vitamin C Deficiency | Notable signs. Scurvy. Gums bleed easily around teeth. Capillaries under skin break spontaneously. |
| Vitamin C Toxicity | Supplementation-based. Diarrhea and GI distress. Also interferes with urine tests. |
| The inability to make enough HCl in the stomach would greatly affect the dietary uptake of which vitamin? | B12 |
| Fat Soluble Vitamins | Vitamins D, E, A, and K. |
| Fat-soluble vitamins require ___ for digestion and absorption. | Bile |
| Fat-soluble vitamins travel through _____ system. | Lymphatic |
| Many _____ vitamins require transport proteins in bloodstream. | fat-soluble |
| Excesses are stored in ______ | Liver and adipose tissue |
| Vitamin A Forms | First fat-soluble vitamin recognized. Three different forms are retinal, retinol, and retinoic acid. |
| Conversion of Vitamin A compounds in food - animal food | Retinyl esters (in animal foods) -> Retinol (supports reproduction) <-> Retinal (participates in vision) -> Retinoic acid (regulates growth) |
| Conversion of Vitamin A compounds in food - plant based | Beta-carotene -> Retinal (participates in vision) -> Retinoic acid (regulates growth) |
| Vitamin ___ is stored in the liver, 1-2 years worth. | Vitamin A! 90% of total Vit A is stored in the liver. |
| Retinol-binding protein (RBP) | Carries vit A in the blood |
| Retinal Function | Vision. In the cornea, helps maintain a crystal clear window. In the retina, makes up photosensitive cells. |
| Rhodopsin is ___ and ____ combined | Opsin and Retinal |
| Retinoic Acid Function | Helps with protein synthesis and cell differentiation. Helps protect skin from sunlight. Helps maintain integrity of mucous membranes. |
| Retinol Function | Helps with reproduction and growth. Helps with bone dismantling for remodel. Beta-carotene is an antioxidant |
| Vit A and Beta Carotene Deficiency | Makes you susceptible to infectious diseases. Causes night blindness. Also can cause xerophthalmia due to lack of vit A in cornea. |
| Vit A and Beta-Carotene Toxicity | Free vitamin A damages cells. Toxicity is real possibility. Children are most vulnerable. Can get from supplements and fortified foods. Causes bone defects. Interferes with Vit D. Cell death from spinal cord. Worsens acne. Antioxidant becomes pro-oxidant |
| Vitamin D Functions | Not essential nutrient. Body synthesizes it via sunlight. Active form is a hormone. Binding protein carries it to target organs. Calcitonin stops absorption. PTH starts it. |
| Vitamin D Deficiency | Overt signs are rare. Insufficiency is common. Creates calcium deficiency. Rickets. Osteomalacia (soft deformed bones). Contributory factors are dark skin, breastfeeding, lack of sunlight, not using fortified milk |
| Vitamin D Toxicity | Mostly due to vitamins, especially in children. Raises blood calcium concentration. May harden blood vessels. Forms stones in soft tissues. Can cause death. |
| Vitamin E Functions | Four different tocopherol compounds. Antioxidant. Protects LDLs and reduces inflammation. |
| Vitamin E Deficiency | Primary deficiency is rare. In secondary deficiency, red blood cells break open. Thrombocytosis and edema. |
| Vitamin E Toxicity | Liver regulates vit E conc. Toxicity is rare. May interfere with vitamin K activity. Hemorrhage. |
| Vitamin K Functions | Acts primarily in blood clotting. Needed for clotting factor activation. Helps in metabolism of bone proteins. |
| Vitamin K Deficiency | Primary deficiency is rare. In secondary deficiency, fat absorption falters. Some drugs disrupt vit K's synth and action (antibiotics and anticoagulants). |
| Major Minerals | Calcium, phosphorus, potassium, sulfur, sodium, chloride, magnesium, iron |
| Trace Minerals | Zinc, copper, manganese, iodine, selenium |
| Inorganic elements | Found on the periodic table of elements. Cannot be destroyed by heat, air, acid, or mixing. Always retain chemical identity. |
| Sodium Functions | Major cation in extracellular fluid. Important in water regulation and acid-base balance. VERY important for nerve transmission. |
| Sodium Excess | Hypertension. Only need 1tsp a day. Bone loss (osteoporosis). Potassium can be protective factor. |
| Sodium Deficiency | Hyponatremia can cause this. |
| Chloride Functions | Major anion of extracellular fluids. Helps maintain fluid and electrolyte balance. Part of HCl. |
| Chloride Deficiency/Toxicity | Rare. Toxicity due to dehydration. |
| Potassium Functions | Principal intracellular cation. Helps maintain fluid and electrolyte balance. Helps with nerve impulse transmission and muscle contraction and cell integrity. |
| Potassium Deficiency | Hypertension. Risk of stroke increased. |
| Calcium Functions | Most abundant mineral in the body. Majority is in bones. Part of bone structure. Helps maintain normal BP. EC helps in blood clotting. IC regulates muscle contraction, helps with nerve impulse transmission, helps in secreting hormones |
| Calcium Deficiency | Osteoporosis. Bones fracture under normal everyday stress. |
| Phosphorus Functions | Second most abundant mineral in the body. Part of major buffer system. Part of DNA/RNA. Assists in energy metabolism. Helps transport lipids in blood. Structural component of cell membranes. |
| Magnesium Functions | More than half found in bones. Maintains bone health. Part of protein making machinery. Necessary for ATP production. Helps with muscle contraction and blood clotting. Supports normal function of immune system. |
| Iron Functions | Too little and too much can be harmful. Switches back and forth between ferrous iron (2+) and ferric iron (3+). Cofactor in redox reactions. Part of electron carriers. |
| Absorption of iron | Ferritin - stored in small intestine. Vitamin C helps iron absorption. |
| Iron Deficiency | Most common nutrient deficiency worldwide, 1.6 billion. Link with being overweight. Happens in stages. |
| Iron Deficiency Stages | 1) Iron stores diminish - serum ferritin 2) Decrease in transport iron - transferrin 3) Iron deficiency - hemoglobin and hematocrit values (once you get to this point, you have anemia) |
| Iron Toxicity | Hereditary hemochromatosis. Most common genetic disorder in US. Hemosiderosis. Deposits in liver, heart, and joints due to iron being released outside of cells. Symptoms similar to iron deficiency. Treatment is iron chelation therapy. |
| Zinc Functions | A lot! Gene expression, cell membranes, immune function, growth and development, synthesis of insulin, blood clotting, thyroid hormone function, visual pigment, taste perception, sperm production |
| Zinc Recycling | Small intestine. Enteropancreatic circulation. |
| Zinc Deficiency | Growth retardation, impaired immune response, damage to CNS |
| Zinc Toxicity | Interference with copper metabolism (leads to heart degeneration) |
| Iodine Functions | Part of thyroid hormones. Body temp, metabolic rate, reproduction, growth, blood cell production, nerve and muscle function, etc. |
| Iodine Deficiency | Thyroid hormone production declines. Can cause goiter or cretinism |
| Iodine Toxicity | Interferes with thyroid function. Enlarged thyroid gland. |
| Selenium Functions | Antioxidant. Part of proteins. Helps convert thyroid hormone to active form. |
| Selenium Deficiency | Heart disease, higher risk of cancer |
| Selenium Toxicity | Loss and brittleness of hair and nails, garlic breath, nervous system abnormalities |
| Copper Functions | Constituent of enzymes, iron metabolism, antioxidant. |
| Copper Deficiency | Cardiovascular disease? Inability to make ATP. Menke's Disease. |
| Copper Toxicity | Wilson's Disease |
| Manganese Functions | Cofactor for enzymes that facilitate metabolism, bone formation, conversion of pyruvate to acetyl-CoA |
| Other Trace Minerals | Nickel, Silicon, Vanadium, Cobalt, Boron |
| Contaminant Minerals | Lead, Mercury, Cadmium |
| _________ and ________ form the smallest and simplest carbohydrates. | glyceraldehyde and dihydroxyacetone |
| Glyceraldehyde exists as __ and __ enantiomers | D and L |
| ___ form of carbohydrates are the most common in the human body | D |
| Aldehydes contain an? | Aldose |
| Ketones contain? | A ketose |
| Epimers | Structure different in one position |
| 5 and 6 carbon sugars can become ______ | cyclic |
| Aldehyde or ketone can react with a ______ | hydroxyl group |
| Pyranose | six sided ring |
| Furanose | five sided ring |
| Alpha confirmation around the anomeric carbon | OH group is pointed in opposite side as the CH2OH group |
| Beta confirmation around the anomeric carbon | OH group is pointed in same side as the CH2OH group |
| Monosaccharides of importance | Glucose Blood sugar Fructose Fruit sugar Sweetest Galactose Sweet but least sweet of the three |
| Disaccharides of importance | Sucrose Table sugar glucose-fructose Lactose Milk sugar Glucose-galactose Maltose Major product of starch degradation Glucose-glucose |
| Glycosidic bonds | Bond that forms between the OH group of an anomeric carbon and another reactive group (usually another OH) |
| Typical glycosidic bond involves the OH group of? | Another sugar |
| Glycosidic bond is named after? | The type of anomer and carbons involved |
| Anomeric carbon | The hemiacetal carbon of a cyclic sugar. A chiral center which results from ring closure upon an aldehyde or ketone in an acyclic sugar |
| Reducing anomeric carbon | Anomeric OH is free and not involved in a glycosidic bond |
| Non-reducing anomeric carbon | The anomeric OH is not free, it is part of a glycosidic bond |
| Homopolysaccharides | 1 type of monomer makes up the polymer Glycogen, starch, cellulose |
| Heteropolysaccharides | 2 or more monomers make up the polymer Glycosaminoglycans, peptidoglycans |
| Describe glycogen. | Major storage form of glucose in the body (especially in the muscle and liver) Polymer of glucose residues linked alpha (1,4) Highly branched every ~4 residues with alpha (1-6) |
| Describe starch. | Major storage form of glucose in plants Polymer of glucose Structure is identical to glycogen but with a lower degree of branching (20-30 residues) Unbranched - amylose Branched - amylopectin |
| Cellulose | Polymer of glucose |
| Describe glycosaminoglycans | Large unbranched saccharide complexes Usually a repeating disaccharide unit Amino sugar (D-glucosamine or D-galactosamine) Acidic sugar (D glucoronic acid or D-iduronic acid) Negative charge (from acid group and additional sulfate groups) |
| Describe glycosaminoglycans | Bind large amounts of water = gel like matrix Viscous/lubricating properties = mucus |
| Glycoconjugates | Biologically active molecules made from a carbohydrate covalently linked to a protein or lipid Glycolipids Glycoproteins and proteoglycan |
| Glycoconjugates are important in? | Cell-cell recognition and adhesion Cell migration during development Blood clotting, the immune response, wound healing, etc |
| The carbohydrate part of glycoconjugates serve as? | The information carrier by providing specific, high affinity recognition sites. |
| Proteoglycan | More carbohydrate than protein Located at the cell surface and ECM Major components of CT, providing strength and resilience |
| Glycoproteins | More protein than carbohydrate Carbohydrate forms a glycosidic linkage with the OH of Ser or Thr through its anomeric end (O-linked), or an N-glycosyl link through the amide of Asn (N-linked) |
| Glycolipids | Carbohydrates attached to lipids on the extracellular surface of the membrane Provide energy Used in cellular recognition for chemicals Provide membrane stability and help attach cells to each other to form tissues |
| The ultimate goal in carbohydrate metabolism | Glucose |
| Glucose provides ___% of brain fuel | 99% |
| Saliva contains _____ which cleaves alpha (1,4) linkages of polysaccharides (starch) | Amylase |
| In the stomach, fibers (indigestible polysaccharides) provide what? | A feeling of fullness |
| HCl in the stomach also aids in? | Digestion |
| Site of the most carbohydrate digestion | Small intestine |
| Specific disaccharide enzymes in the small intestine | Maltase Sucrase Lactase |
| Fibers in the large intestine do what? | Attract water and ferment to short chain fatty acid |
| Liver storage of glucose? | Stores as glycogen. 1/3 of body's glycogen. Lasts hours. Glucose storage for all cells in the body. |
| Muscle storage of glucose | Stores as glycogen. 2/3 of body's glycogen. Selfishly hoards glycogen and releases glucose only for itself |
| Every cell in the body can use _______ | glucose |
| What is preferred source for brain, nerve cells, and developing red blood cells? | Glucose |
| Cellular breakdown of glucose (glycolysis) | Aerobic - glucose is oxidized to pyruvate Anaerobic - glucose is oxidized to lactate Eventually, complete breakdown = CO2 and H2O |
| Gluconeogenesis | New glucose making |
| Glycolysis occurs in? | Cytoplasm of all cells |
| The two phases of glycolysis | Energy-Investment Energy-Payoff |
| Energy-Investment uses ___ ATP for chemical reactions | 2 |
| Energy-Payoff builds? | 4 ATP and 2 NADH |
| Net payout of glycolysis | 2 ATP, 2 NADH, and 2 pyruvate (in aerobic) |
| Why do we use ATP in glycolysis? | Because we need one of those phosphates |
| Glycolysis Reaction 1 | Hexokinase puts a phosphate on glucose. Glucose turns into glucose-6-phosphate. |
| Glycolysis Reaction 2 | We have Glucose-6-phosphate. Phosphoglucose isomerase changes G6P into Fructose-6-phosphate. This reaction is reversible. |
| Resting glucose concentration in the blood | 5mmol. Only time that really goes up is when we eat |
| Glycolysis Reaction 3* | Starting with fructose-6-phosphate. Phosphofructokinase-1 adds a phosphate group to the 1 and 6 carbons, making it Fructose-1,6-biphosphate. THIS IS THE RATE DETERMINING STEP. It is the slowest step. Not readily reversible. |
| Glycolysis Reaction 4 | Starting with fructose-1,6-biphosphate. Aldolase takes it and slices it and turns it into dihydroxyacetone phosphate and glyceraldehyde-3-phosphate. (3-carbon carbohydrates with some phosphates on them). This is reversible. |
| Glycolysis Reaction 5 | Starting with dihydroxyacetone phosphate and glyceraldehyde-3-phosphate (GAP). Triose phosphate isomerase converts DHAP and GAP. Only GAP is used in the rest of glycolysis. Last step of phase 1. |
| Glycolysis Reaction 6 | GAP is oxidized and phosphorylated by glyceraldehyde-3-phosphate dehydrogenase. This creates 1,3-biphosphoglycerate. This is when NADH is generated. This is reversible. |
| Whenever you see dehydrogenase, 99% of the time it has something to do with? | Converting NAD+ into NADH or backwards. |
| Oxidation of GAP results in? | The reduction of NAD+ to NADH. |
| Heavy metals like lead, mercury, cadmium, etc love to bind to ______. This can cause a problem in ______. | cysteines. This can cause a problem in GAP dehydrogenase. Renders the enzyme nonfunctional. |
| Glycolysis Reaction 7 | Phosphate is added to ADP. ATP generated by phosphoglycerate kinase during the conversion of 1,3-BPG to 3-phosphoglycerate. This is reversible. |
| Glycolysis Reaction 8 | The most boring reaction of glycolysis. Conversion of 2-phosphoglycerate into 3-phosphoglycerate. Isomerase reaction. Enzyme is phosphoglycerate mutase. |
| Glycolysis Reaction 9 | At a point when we need to make a molecule that will help us make ATP later on. Take 2PG and dehydrate it via enolase* to form phosphoenolpyruvate (PEP). This also generates a water molecule. |
| Reactions of Glycolysis that generate ATP | Reaction 7 and 10 |
| Glycolysis Reaction 10 | Generating ATP. Pyruvate kinase transfers phosphate from PEP to ADP, generating pyruvate and ATP. Mostly irreversible. |
| In glycolysis we do two #___'s and two #____'s, which is how we generate 4ATP total. | #7s and #10s |
| What is the function of a mutase? | Causes relocation of functional groups |
| By consuming fructose and using it, you can skip what? | All the beginning steps of glycolysis. You bypass two regulatory steps by intaking fructose. Like high fructose corn syrup. |
| In oxygenated conditions, pyruvate goes into? | The TCA cycle |
| In deoxygenated conditions, pyruvate is converted into? | Ethanol |
| Humans, under anaerobic conditions, convert pyruvate to? | Lactate |
| Fermentation generates only __ATP because fermentation is? | 2 ATP because fermentation IS glycolysis. |
| If you get plastered, your ability to do _______ gets slowed down | glycolysis |
| Cori Cycle | Any lactate that is generated is not wasted. It takes extra lactate to the liver where it is converted back to glucose |
| The three enzymes for regulating glycolysis | Hexokinase, phosphofructokinase 1, and pyruvate kinase |
| Phosphofructokinase 1 | Glycolysis regulating enzyme. Presence of ATP inhibits this enzyme. Presence of citrate does too. Regulated by glucagon. ADP and AMP can enhance PFK1 to the point where it override whatever amount ATP is inhibiting. |
| The more negative delta G, the ______ a reaction is going to occur in one direction. | More |
| In a fasting state, your blood glucose levels are ____. You release _______ during this state. This affects what cells? | Blood glucose levels are low. You release glucagon during this state. This only affects liver cells. |
| In a fasting state, the liver activates an enzyme called ______, which does what to PFK2? | Activates protein kinase A. It phosphorylates PFK2. This inhibits PFK2 from making F2,6BP. This stops glycolysis. |
| In a fed state, your blood glucose levels are _____. You release ____ during this state. What does this activate? | Your blood glucose levels are high. You release insulin during this state. This activates protein phosphatase 1. This removes the phosphate that was added to PFK2, which restarts glycolysis. |
| 95% of the time, if insulin is around, it will lead to phosphatase, so we ____________ things. | Dephosphorylate |
| Whenever glucagon is around, this activates PKA, which __________ things. | Phosphorylates |
| If there's a lot of ATP or CoA, pyruvate will be _______ | Inhibited |
| F1,6BP stimulates? | Pyruvate kinase |
| Describe the 2,3 BPG shunt. | Biphosphoglycerate mutase converts 1,3BPG to 2,3BPG. This is important for knocking oxygen off of hemoglobin molecules. This shunt means you bypass part of glycolysis. |
| Describe the pentose phosphate shunt. | Ribulose 5-phosphate. Used to generate ribose 5-phosphate, the precursor to making nucleotides. |
| Tricarboxylic acid cycle only happens if? | Oxygen is around |
| Three metabolic fuels for TCA | Sugars, fatty acids, amino acids/proteins |
| We need acetyl-CoA to enter into the TCA cycle. After glycolysis, we have __________. We need _____ to change that. | We have pyruvate. Pyruvate dehydrogenase changes that. |
| Advantages of multienzyme complexes | The distance that substrates have to diffuse is decreased (less traveling). This enhances reaction rate. The intermediates are never exposed to the outside environment. They never get lost! Most important advantage - if you control one, you control all. |
| Five coenzymes needed for pyruvate dehydrogenase | E1: Thiamine pyrophosphate E2: Lipoamide pathotenic acid E3: riboflavin NAD+: nicotinamide |
| General Features of TCA | Starts with oxaloacetate, adds two carbons from caetyl CoA, and generates citric acid |
| TCA occurs where? | In the mitochondria |
| A molecule made in the TCA cycle can be used to make ________ | glutamate |
| TCA Reaction 1 | Citrate synthase combines oxaloacetate and acetyl to generate citrate. |
| TCA Reaction 2 | The enzyme aconitase changes citrate into isocitrate. |
| TCA Reaction 3 | Isocitrate dehydrogenase chops off a carbon and generates alpha-ketoglutarate. Also generates an NADH molecule |
| TCA Reaction 4 | Alpha-ketoglutarate dehydrogenase converts alpha-ketoglutarate into succinyl-CoA. Generates another NADH molecule. Leftover carbon is added to CoA. |
| TCA Reaction 5 | Succinyl-CoA is generated into succinate by Succinyl CoA synthetase. GTP is converted into an ATP molecule by the enzyme nucleoside diphosphate kinase. |
| TCA Reaction 6 | Succinate dehydrogenase generates FADH2. Converts succinate and converts it into fumarate. The enzyme can take the electrons it just took from succinate and give them to the electron transport chain. |
| TCA Reaction 7 | Most boring reaction of TCA. Conversion of fumarate into malate. You use water and fumarase to do it |
| TCA Reaction 8 | Oxaloacetate is regnerated by malate dehydrogenase. Allows for cyclic nature. |
| Products of the TCA per cycle | 3 NADH 1 FADH2 A GTP --> ATP 2CO2 |
| Which of the TCA steps is also a component of the electron transport chain? | Succinate to fumarate |
| Biggest regulator of TCA | pyruvate dehydrogenase. Regulates how much acetyl-CoA is actually entering into the cycle itself. Without the phosphate, PDH is active. Add a phosphate and it will shut off, which restarts the cycle. |
| Anaplerotic reactions make? | TCA intermediates |
| Fluoroacetate | Pesticide. Binds easily to CoA and forms fluoroacetyl-CoA. This binds to aconitase as a competitive inhibitor, which stops TCA |
| Arsenate | Can bind to sulhydryl compounds and not allow other things to bind |
| Describe mitochondria | Has smooth outer membrane with no divots, then highly folded inner membrane. Within the cristae are all enzymes required for electron transport. Foldings increase surface area. Very interior = matrix |
| TCA enzymes are found where? | In the mitochondrial matrix. One of them is found in the inner membrane (succinate dehydrogenase) |
| All enzymes required for fatty acid oxidation are found where? | In the mitochondrial matrix |
| All enzymes involved in ETC and oxidative phosphorylation are found where? | In the inner membrane and inner membrane space of mitochondria |
| Anything that's about _______ daltons can pass through the outer membrane. | 1,000 |
| Two pathways to get NADH into the mitochondria | Malate-aspartate shuttle (more ATP per NADH) and glycerol phosphate shuttle |
| Describe the malate-aspartate shuttle | NADH synthesis is possible within the matrix after oxaloacetate interacts with NADH, causing conversion to malate. It is converted back to oxaloacetate inside by reducing NAD+. |
| Describe the glycerol phosphate shuttle | NADH reacts with dihydroxyacetone phosphate (DHAP), which gives us NAD+ and glycerol-3-phosphate. The electrons go directly into the ETC. |
| Lipid soluble electron carrier | Coenzyme Q (ubiquinone) |
| Water soluble electron carrier | cytochrome c (protein) |
| Electrons will pass freely from a molecule that has a _______ redox potential to a molecule that has a ________ redox potential. | From lower to higher |
| Redox potential (midpoint potential) | The point at which half of the molecules are reduced and half are oxidized. |
| Cofactors and Prosthetic Groups of ETC | NADH, FMN, FADH2, CoQ, Fe-S, and heme |
| Protein complexes of the ETC | Complex I, II, and III |
| Describe NADH in ETC | Redox reaction. Free water soluble electron carrier. 2 electrons are transferred. Often the first step in the ETC is oxidation of NADH to NAD+. |
| Describe FMN and FADH2 in ETC | Water soluble, protein-bound electron carriers. 1 or 2 electrons can be transferred. Can generate a semiquinone. <- Most of these are radicals |
| Describe CoQ in ETC | Free lipid-soluble electron carrier. 1 or 2 electrons can be transferred. Found inside the hydrophobic region of the inner membrane of mitochondria. May generate a semiquinone. |
| Describe iron-sulfer cluster (Fe-S) in ETC. | Protein-bound electron carrier. 1 electron is transferred. Electron is transferred to sulfer which is then stabilized by iron. Many are bound together via cysteine residues. |
| Describe heme in ETC. | Protein-bound electron carrier. 1 electron is transferred. Consists of a large porphyrin ring and Fe atom in the center. There is Heme A, B, and C |
| Heme A | Has a big hydrophobic carbon tail |
| Heme B | Is the type of heme you find in hemoglobin molecules |
| Heme C | Becomes covalently bound to the protein that has it |
| Describe Complex I of ETC. | FMN accepts electrons from NADH. Electrons are given to CoQ. Protons are going from the matrix to the innermembrane space. |
| Describe Complex II of ETC. | Accepts electrons. Also present in TCA cycle. Electrons go from FAD, thru Fe-S, thru heme, and eventually given to CoQ. So, electrons go from succinate to CoQ. Electron transfer is NOT coupled with proton translocation here. |
| Complex I and II do not work in series but accomplish the same result, which is? | Reducing CoQ. |
| Describe Complex III of ETC. | Passes electrons from reduced CoQ to cytochrome c. Electrons ultimate given to cytochrome C AND back on Q. Electron transport bifurcates at this point. |
| What is the final acceptor in the electron transport chain? | Oxygen |
| Which Complexes in ETC use passage of electrons to translocate protons from the matrix to IMS? | Complex I, III, and IV (NOT II) |
| Describe Complex V of ETC. | Very large. Has two parts, water-insoluble and water-soluble. Has a lollipop appearance. Works as if it's a rotary engine. |
| What if you put a dam in the ETC? | On the earlier side, everything is reduced. On the other side, everything is oxidized. |
| Describe Rotenone | A plant toxin used by Amazonion Indians to poison fish. Also used as an incesticide. Blocks electron transport in Complex I. |
| Antimycin A | A piscicide which blocks electron transport in Complex IV. Doesn't allow oxygen to be converted into water. Stops electrons from going to their final acceptor. |
| Oligomycin blocks which complex of ETC? | Complex V |
| If you shut down Complex II, will the ETC continue? | No. Because Complex II is part of the TCA cycle, and the big thing you make in TCA cycle is NADH. If you don't have NADH, there's no substrate to start Complex II. The whole thing would shut down. |
| Uncoupling in brown adipose tissue generates ______ | Heat |
| Describe 2,4-dinitrophenol (DNP). | This was used as a diet pill in the 1920s, which was effective but often caused fatal side effects. People would die of temperatures at 107 degrees Fahrenheit. You can get DNP in Mexico. |
| Uncouplers keep ETC from making ______ | ATP |
| How do you make salmon taste less fishy? | If you remove the brown adipose tissue, you get rid of the fishy taste |
| Partial oxygen reduction produces? | Reactive oxygen species |
| Cells are equipped with _______ mechanisms. | antioxidant |
| Superoxide dismutase | Takes superoxide and converts it into hydrogen peroxide and oxygen |
| Catalase | Takes H2O2 and converts it into water and oxygen. This is the bubbling when you pour H2O2 on a wound. |
| Glutathione Peroxidase | Takes H2O2 and converts it into water. |
| Liver and muscle store glucose as? | Glycogen |
| Liver glycogen is used for? | Whole body, and maintaining blood glucose levels |
| Coma can result if blood glucose falls below ________ | 2.5mmol/L or 45mg/dL |
| Muscle glycogen is for? | Only muscle cells |
| Glycogen can have up to ____________ glucose units | 120,000 |
| Glycogen synthesis occurs around a? | Protein core (glycogenin) |
| Glycogen utilization proteins are found where? | On the surface of the molecule |
| Glycogen is made up of glucose molecules stuck together in what linkages? | Alpha 1,4 linkages |
| The three major steps of glycogen synthesis | Conversion of G6P to G1P The addition of UDP to Glucose The addition of glucose units to growing glycogen chain (including branching) |
| With glycogen synthase, the glucose units are transferred to? | To the C4 of the non-reducing end of a glycogen chain |
| In glycogen synthesis, the release of UDP from the glucose unit forms a? | Highly reactive oxonium ion intermediate |
| Glycogenolysis supplies blood glucose once levels are below? | 5mmol/L |
| Most important step of glycogenolysis | G1P is removed from glycogen chain via glycogen phosphorylase. The alpha 1,4 linkage is broken and this breaks the bond between the glucose unit and the rest of the glycogen molecule. |
| In glycogenolysis, the conversion of G6P to glucose happens where? | ONLY in the liver. Done by glucose phosphatase. This step using a debranching enzyme. After breaking the bonds, the remaining glucose of the branch is removed by a glucosidase* |
| Regulation of glycogen metabolism is done via __________ control. | Allosteric |
| Glycogen Phosphorylase is activated by ______ and inhibited by _______. | Activated by AMP and inhibited by ATP and G6P. |
| Glycogen synthase is activated by _____. | G6P. |
| When glycogen synthase is phosphorylated, it is __________. When glycogen phosphorylase is phosphorylated, it is __________. | When phosphorylated, it is INACTIVATED. When glycogen phosphorylase is phosphorylated, it is ACTIVATED. |
| The pancreas creates both ________ and ________ for us. | insulin and glucagon |
| Glucagon only communicates with _______ cells, telling it to release the glycogen stores. | liver |
| What is PP1i? | Protein phosphatase 1 inhibitor. |
| Phosphorylase kinase becomes SUPER activated when it binds to __________. | Calmodulin |
| Calmodulin needs to bind to _______ in oder to be activated. | calcium |
| We need _______ in order for our glycogen to be optimum | calcium |
| In a fasting state, which hormone is released? What increases directly because of that? | Glucagon is released. Cyclic AMP increases, which causes an increase in PKA. |
| In a fasting state, once PKA is increased, this phosphorylates what? What does that do? | PFK2, which decreases the synthesis of F26BP, so PK1 activity goes down, stopping glycolysis. |
| When in a fed state, what hormone is activated? What does that directly affect? | Insulin is released. This activates PP1, which dephosphorylates PFK2. |
| In a fed state, once PFK2 is dephosphorylated, what happens? | This causes an increase in F26BP, which activates PFK1 and activates glycolysis |
| Von Geirke's | Glycogen Storage Disorder. Type Ia is most common. Hepatomegaly, kidney failure, and thrombocyte dysfunction. Liver-only. Problem with G6phosphatase. Enzyme is dysfunctional. Accumulation of G6P in the endoplasmic reticulum. |
| Pompe's | Glycogen storage disorder. Affects lysosomal acid glucosidase. Affects skeletal and cardiac muscle. Fatal by 2 years old if infantile. Myopathy and musclar dystrophy. Defects in glycogen degradation in lysosome. Glycogen accumulates. |
| Cori's and Forbe's | Glycogen storage disorder. Affects the debranching enzyme. Affects liver and/or muscle. Infant hepatomegaly, myopathy. Cannot use glycogen to full extent. Accumulation of branched glycogen. |
| Anderson's | Glycogen storage disorder. Affects branching enzyme. Affects liver and/or muscle. Hepatomegaly and splenomegaly. Cirrhosis. Accumulation of glycogen with few branch points. Death due to cardiac or liver failure in first year of life. |
| McArdle's | Glycogen storage disorder. Problem in skeletal muscle only. Muscle phosphorylase issue. Cannot break down glycogen very well. Cramps, muscle pains, etc on exertion. |
| Her's | Glycogen storage disorder. Failure of the liver phosphorylase. Accumulation of glycogen in the liver. Hepatomegaly. Affects just the liver. |
| Vitamin Pills Can Anger Mr. Horn | Von Geirke's, Pompe's, Cori's and Forbe's, Anderson's, McArdle's, Her's |
| Which GSD would result in a buildup of G6P in the liver cell? | Type Ia - Von Geirke's |
| Starting substrates in gluconeogenesis | Pyruvate and lactate; any of the TCA cycle products; proteins (except for leucine and lysine) |
| Steps of gluconeogenesis | Conversion of pyruvate to oxaloacetate Formation of PEP from oxaloacetate Formation of F6P from F1,6BP Glucose made by dephosphorylation of G6P |
| ________ is a cofactor of pyruvate carboxylase (involved in gluconeogenesis step 1) | Biotin |
| The last step of gluconeogenesis occurs in? | Only in the liver. |
| The two control mechanisms of gluconeogenesis regulation | Acetyl-CoA. Makes pyruvate carboxylase increase if there's a lot of it. Starts making more glucose. F2,6BP will cause glycolysis instead if there's a lot of it. |
| Functions of lipids | Energy storage Insulation from environment Water repellant Membrane structure Cofactors for enzymes Signaling molecules Pigments Antioxidants |
| Vitamin K is a cofactor in? | Blood clot formation |
| Coenzyme Q is a cofactor in? | ATP synthesis in mitochondria |
| How do paracrine hormones work as signaling molecules? | They act locally |
| How do steroid hormones work as signaling molecules? | They act widely - across the body |
| Vitamins __ and __ are hormone precursors | A and D |
| Vitamin __ is an antioxidant. | E |
| Does cholesterol contain fatty acids? | Nope |
| Structure of triacylglycerols | Glycerol with three fatty acids. Is a storage lipid. |
| Structure of glycerophospholipids | Glycerol with two fatty acids and a PO4/alcohol group. Is a phospholipid. |
| Structure of sphingolipids | Is a sphingosine with a fatty acid and a PO4/choline group as a phospholipid Is a sphingosine group with a fatty acid and a mono or oligosaccharide group as a glycolipid. |
| Structure of galactolipids | Glycerol with two fatty acids and a mono or disaccharide and SO4 group. This is a glycolipid. |
| Fatty acids are ______ acids with hydrocarbon chains containing between __ and __ carbons | are carbodylic acids containing between 4 to 36 carbons. |
| Almost all fatty acids have a ____ number of carbons. | Even number |
| Most naturally fatty acids are branched/unbranched | unbranched |
| Describe a saturated fatty acid | No double bonds between carbons in the chain, ex stearic acid |
| Describe a monounsaturated fatty acid | One double bond between carbons in the alkyl chain, ex oleic acid |
| Described a polyunsaturated fatty acid | More than one double bond in the alkyl chain, ex linoleic acid and alpha-linolenic acid |
| Can humans synthesize omega-3 fatty acids? | Nope |
| A steroid nucleus is made up of? | Four fused rings |
| Sterol makeup | Steroid nucleus Hydroxyl group (polar head) in the A ring Various nonpolar side chains The steroid nucleus is almost planar |
| Cholesterol will cause a membrane to be _____ when it's cold and ______ when it's warm. | Cause a membrane to be more fluid when it's cold and more solid when it's warm. |
| Arachidonic acid derivatives as signaling lipids | Enzymatic oxidation of arachidonic acid yields prostaglandins (inflammation and fever) thromboaxanes (formation of blood clots) leukotrienes (smooth muscle contraction in the lungs) |
| Oxidation of _______ is a major energy source in many organisms | fatty acids |
| About ___% of energy needs of mammalian heart and liver are met by oxidation of fatty acids | 80% |
| Fats are degraded into _______ and ______ in the cytoplasm of adipocytes | Fatty acids and glycerol |
| Beta-oxidation of fatty acids occurs in the _________. | Mitochondria |
| ________ activates glycerol at the expense of ATP | Glycerol kinase |
| Stages of fatty acid oxidation | -Conversion of two-carbon units into acetyl-CoA via beta-oxidation with noncomitant generation of NADH and FADH2 -Oxidation of acetyl-CoA into CO2 via citric acid cycle with concomitant generation NADH and FADH2. -Generates ATP from NADH via resp chain |
| Beta-Oxidation Pathway | Each pass removes one acetyl in the form of acetyl-CoA. Keeps happening until there are only 4 carbons. With 16-carbon fatty acid, this happens 7 times and 8 CoA's are generated. 7 NADHs as well. |
| Naturally occurring unsaturated fatty acids contain ________ bonds. | cis double bonds. |
| Catabolism of fatty acids | Produces acetyl-CoA Produces reducing power (NADH) Takes place in the mitochondria |
| Anabolism of fatty acids | Requires acetyl-CoA and malonyl-CoA Requires reducing power from NADPH Takes place in cytosol in animals |
| Malonyl-CoA is formed from? | acetyl-CoA and bicarbonate |
| Synthesis of fatty acids is catalyzed by? | Fatty acid synthase |
| Overall goal of fatty acid synthesis | Attach two C-acetate units from malonyl-CoA to a growing chain and then reduce it |
| Fatty acid synthesis is tightly regulated via? | ACC (acetyl CoA carboxylase) |
| Citrate signals excess energy to be converted to? | Fat |
| When we make a lot of acetyl-CoA, that creates a lot of ______, so extra is sent to make fatty acids. | citrate |
| Cholesterol is the basis for Vitamin ___ and a couple other fat-soluble vitamins | D |
| Bile acids such as _____ emulsify fats. | taurocholic |
| Cholesterol and other lipids are carried on what? | Lipoprotein particles |
| Four major classes of lipoprotein particles | Chylomicrons Very low-density lipoproteins Low-density lipoproteins High-density lipoproteins -smallest, most dense |
| You can take a sample of a protein, look at what the protein component is, and from that you can determine? | What the lipoprotein was overall |
| Chylomicrons do what? | Carry fatty acids to tissues |
| Chylomicron remnants deposit their cholesterol where? | In the liver |
| VLDLs transport what? | Endogenous lipids |
| Mutated LDLs do what? | Cause increased levels of heart attack |
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