Biochemistry Quiz I, Biochemistry Midterm
Electrophoresis
A process where DNA fragments are separated according to size using electrical charges Larger fragments at the top and small fragments at the bottom
While studying a cloned and expressed domain of a protein using circular dichroism, the peptide is found to form an a-helical structure more rapidly in 50% ethanol than it does in water. Which of the following is the best explanation for this difference? A. Competition for hydrogen bonding is lower for ethanol than it is for water B. Ethanol forms covalent interactions with the protein C. Hydrophilic forces are greater in ethanol than in water D. The peptide aggregates in water but not in ethanol van der Waals interactions are lower in ethanol than in water
A. Competition for hydrogen bonding is lower for ethanol than it is for water
What is cyanide poisoning?
Affects cytochrome C in electron transport chain which is needed to make ATP.
Which of the following is coenzyme in nearly every carboxylation reaction? A. B1 B. B2 C. B3 D. B5 E. B7 F. B12
Answer E - B7, biotin. Carboxylation = addition of a CO2 group
To test for a deficiency of plasma protein, a super-specialized cationic stationary phase was designed for chromatography. Which of the following least readily exited the column? A. Cationic protein B. Anionic protein C. Large protein D. Small protein
B. Anionic Protein
Which of the following compounds decreases permeability of membrane lipid bilayers to small water-soluble molecules and enhances both the flexibility and the mechanical stability of the bilayer? A. Gangliosides B. Glycoproteins C. Cholesterol D. Inositol phospholipids E. Neutral glycolipids
C. Cholesterol
membrane cholesterol function
Decreases the mobility of the phospholipid heads and maintains the fluidity of the tail
A male infant is diagnosed with phenylketonuria on newborn screening. Which of the following amino acids must be present in his diet to prevent a negative nitrogen balance? A. Alanine B. Cysteine C. Glutamine D. Serine E. Tyrosine
E. Tyrosine
G1 phase of cell cycle
First phase of cell cycle in which a cell grows and carries on normal metabolic processes
Amino acids act as neurotransmitters. Which amino acid plays a part in Chinese Restaurant Syndrome?
Glutamate
Proteins are often analyzed quantitatively by their absorption of light at 280 nm based on the presence of which of the following amino acids? A. Arginine B. Cysteine C. Histidine D. Leucine E. Methionine F. Proline G. Serine H. Tryptophan
H. Tryptophan
What type of hemoglobin does a baby with B-Thalassemia have?
HbA2 with 2 alphas and 2 deltas
HbC
HbC is also genetic - Glu replaced with a lysine. No signs of negative symptoms because of the polar switch.
HbSC
HbSC is when have allele for both sickle cell and Hbc. Not as severe as full blown HbS, but can still sickling crisis. Usually happens during childbirth or surgery.
Tertiary structures involved several different types of bonding interactions to make its shape. What is the most important interaction that gives the structure its shape?
Hydrophobic interactions. This folding puts the hydrophobic molecules on the inside of the structure and the hydrophilic around the outside.
Summary of Antibodies
IgA - primary response in mucosa IgE - Allergies IgD - B-cells (receptor) IgG - secondary response - can cross placenta IgM - primary response
Which amino acid destabilizes an alpha-helix structure?
Proline (P)
Hydrolysis
The addition of hydrogen to breakdown molecules into smaller units
Answer C - Uncompetitive inhibition might be the easiest to recognize, due parallel lines. In addition to the MM equation, make sure you understand Line-Weaver Burk plots. Remember this: x-intercept = -1/Km & Y-intercept = 1/Vmax. For uncompetitive inhibition, there is an (apparent) decrease in Km and decrease in Vmax. A - Increased Km, Vmax no change B - Vmax decreased, Km no change D - Increased Km, Decreased Vmax - Mixed inhibitors are ideal drugs (in most circumstances) E - inhibition occurs via covalent bonds and is IRREVERSIBLE (aspirin works this way)
The following graph represents addition of which inhibitor? A. Competitive B. Noncompetitive C. Uncompetitive D. Mixed E. Suicide
B. Ser, Asn, Tyr
The following image represents a top, horizontal cross-section of a GLUT2 receptor, located on the plasma membrane of an enterocyte. Which amino acids would you expect to see at the locations marked (?) ? A. Lys, Asp, Glu B. Ser, Asn, Tyr C. Val, Ile, Leu D. Trp, Phe, Arg
B and D
The following is a titration curve of a non-polar amino acid. Which point(s) represents a region of maximum buffering?
What aromatic amino acid is linked to vitamin B3 Niacin?
Tryptophan
SDS-PAGE electrophoresis
denatures the proteins and masks the native charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel. Larger towards the top and smaller towards the bottom
What is a beta-hairpin?
two anti-parallel beta-sheets connected by a b-turn. This is considered a form of secondary super structure.
Structure of a Biological Membrane
-Double layer of phospholipids - Glycoprotein receptors - Integral proteins - Peripheral proteins - Cholesterol - Protein channels The more double bonds (unsaturation) of the fatty acids of the phospholipid tails will make the membrane more fluid.
ion exchange chromatography
-stationary phase is made of either negatively or positively charged beads (attract & bind compounds that have opposite charge) A cation matrix will attract negatively charged particles An anion matrix will attract positively charged particles -salt is added to elute proteins stuck to column
What are the functions of membrane proteins?
1. recognition 2. Structural support 3. Communication 4. Transport
Which of the following shifts the hemoglobin dissociation curve to the left? A. Hypothermia B. Intense exercise C. Staph infection D. Increased 2,3-BPG E. Acidemia
A. Hypothermia Answer A - Hypothermia is a decrease in body temperature, which would shift the hemoglobin curve left. You'll need to have the factors shifting a hemoglobin curve memorized. Try to remember all the factors that will shift the curve right (increase in temp, pCO2, 2,3-BPG; & decrease in pH). A rightward shift represents a decreased in affinity for O2.
What is the structure of an amino acid?
Amino group (N-terminus), Carboxyl group (right side), Side chain (R-group)
A patient comes into your clinic with a complaint of loose stools. They seem confused about how long its lasted. Physical examination shows severe inflammation of the skin. Which vitamin could help these symptoms? A. Vitamin B1 B. Riboflavin C. Niacin D. Thiamine E. Folic acid F. Vitamin C
Answer C - Vitamin B3, niacin deficiency is categorized as the 4D's - Diarrhea, Dermatitis, Dementia, and finally, Death.
Which of the following forms of Hemoglobin is used in blood tests for diabetes? A. HbA B. HbF C. HbC D. HbD E. HbA1c
Answer E - Increased levels of HbA1c in blood is associated with diabetes due to increased glucose in the bloodstream. Increased blood glucose causes HbA to become glycosylated. Thus, an increase [HbA1c] indicates high glucose levels and potential diabetes. This test is typically a follow up to a positive glucosuria test.
An amniocentesis shows increased α-fetoprotein in amniotic fluid collected from a young mother. This is indicative of a neural tube defect caused by deficiency of which of the following? A. Scurvy B. Thiamine deficiency C. Collagen mutation D. Riboflavin deficiency E. Folate Deficiency
Answer E - Neural tube defects can be caused by folate (B9) deficiency. You'll learn about amnios in EHD (hint: important for NBME).
A dietary deficiency of vitamin C would result in: A. Decreased extracellular cleavage of procollagen B. Increased extracellular cleavage of pro collagen C. Increased extracellular cleavage of elastin D. Increased hydroxylation of Pro & Lys in pro collagen E. Decreased hydroxylation of Pro & Lys in pro collagen F. Beri beri
Answer E - vit C deficiency is scurvy. Make sure you know the steps of collagen biosynthesis!
A neonatal nurse notices that the urine produced by a newborn infant has the odor of maple syrup. What biochemical reaction is most likely defective? A. Metabolism of aromatic amino acids B. Metabolism of branched-chain amino acids C. Metabolism of sulfur-containing amino acids D. One-carbon transfer reactions E. Transformation of carbohydrates to amino acids
B. Metabolism of branched-chain amino acids Some of the test questions you may receive seem like they involve things that you have not learned yet, however you can usually easily answer the question by critically thinking and getting to the answer. So the infant has an odor that smells like maple syrup. This can only be one disease which we have covered.
A 45-year-old woman developed dementia, myoclonus, weakness and spasticity. She became comatose within months after onset of neurological signs. Postmortem brain biopsy showed spongiform encephalopathy consistent with Creutzfeldt-Jakob disease. Several encephalopathies including Creutzfeldt-Jakob are thought to be caused by prions. What level of protein structure is altered by prions? A Primary structure B. Secondary structure C. Tertiary structure D. Quaternary structure
B. Secondary Structure If you skimmed through it really fast (the symptoms are not important because it tells you what disease she has), you will see that she has a prion disease. A prion is a misfolded protein that and infects other proteins causing them to misfold
What does carbon monoxide do?
Binds to haemoglobin in the blood which reduces the efficiency of delivering the blood around the body. Changes the color of the blood to Cherry red. Can lead to fainting, coma, or death
What group of amino acids are known to cause Maple Syrup Disease?
Branching amino acids. Valine, Luecine and Isoluesine
Which of the following is not a characteristic of facilitated diffusion? A. Saturation B. Passive diffusion C. Co-transport D. Movement down an electrochemical (EC) gradient E. Carrier-mediation
C. Co-Transport Answer C - co-transport is when one molecule moves across a membrane along with another molecule moving down its EC gradient. This is considered secondary active transport A - the carrier proteins involved in facilitated diffusion can become saturated
Which of the following is most likely to be found in the primary sequence of a protein permitting the transition from an a-helix to b-pleated sheet? A. K B. M C. E D. P E. Y F. G
D. P Answer D - Proline (P) destabilizes a-helices, and thus is not found in turns of a-helices; however, it is often found at the end of helices when transitioning to another secondary structure. This same reasoning is applied for b-turns.
Which of the following would result in a cell membrane with the most fluidity? A. Saturated lipids with long tails B. Saturated lipids with short tails C. Unsaturated lipids with long tails D. Unsaturated lipids with short tails
D. Unsaturated lipids with short tails
A 42 year-old woman comes to the neurologist for enrollments in a research study. She has a 15 year history of resting tremor, bradykinesia, and cogwhee rigidity consistent with Parkinson's disease. One of her siblings recently started having similar symptoms. Genetic analysis is performed on the patient and her affected sibling. The results show a loss of function mutation in a gene that leads to the accumulation of mis-folded proteins. Which of the biochemical processes is most likely defective in this patient? A.) Aceylation B.) Gamma-carboxylation C.) Glucuronidation D.) Phosphorylation E.) Ubiquitination
E) Ubiquitination This question is a typical type of question you'll get on a test. It will be a very drawn out question with a lot of excess information that is not necessary for the question. Many students may see this question and gets scared and start focusing on all the unnecessary details, but usually we only need one or two
What is eastern plotting?
Used for plotting DNA
G0 phase of cell cycle
a non dividing stage in which the cell is metabolically active
What frequency does aromatic groups absorb light?
280 nm
Which of the following has an important role in a type 1 hypersensitivity allergic reaction? A. IgA B. IgE C. IgD D. IgG E. IgM
Answer B - We had a question on this, I believe it was IgE. Either way, if you get a question on these, it'll be easy just remember these: IgA - primary response in mucosa IgE - Allergies IgD - B-cells IgG - secondary response - can't cross placenta IgM - primary response
Methanol poisoning can cause blindness and severe liver damage. As a competitive inhibitor, methanol binds alcohol dehydrogenase and: A. Lowers its Km; no effect on Vmax B. Lowers its Vmax; no effect on Km C. Increases its Km; Decreases Vmax D. Increases its Km; no effect on Vmax E. Both Km and Vmax are decreased
Answer D - Standard kinetics question. Make sure you know how each inhibitor affects Km and Vmax. Remember: a higher Km results in weaker binding affinity. A - This would be an enhancer! B - Non-competitive C - Mixed D - Competitive E - Uncompetitive
Beta sheets are formed by hydrogen bond just like alpha helix structures. For beta sheets, what is the most stable type of beta-sheet?
Anti-parallel because they make three hydrogen bonds, while parallel only make two.
A group of researchers is studying the pathogenesis of Alzheimer disease. A protein isolated from brain tissue of an effective patient has mostly now for healing structure. A sample of a new medication is applied to the protein in the prevailing structure changes to beta pleated sheet. This conformational change is a result of reorganization and which of the following A.) Ionic interactions B.) Hydrophobic interactions C.) Peptide Bonds D.) Hydrogen Bonds E.) Disulfide Bonds
D) Hydrogen Bonds This question is simply asking what bonds are involved and secondary structures. Ignore all the fluff and try to figure out what the question is really asking. A drug is changing one secondary structure to a different secondary structure, which means it must be breaking a bond involving secondary
Dehydration
The removal of a hydrogen bond to link two monomers together.
S phase
The synthesis phase of the cell cycle; the portion of interphase during which DNA is replicated.
What is northern plotting?
Used for plotting RNA
What comprises HbA?
two alpha and two beta
What is Sickle Cell Disease (HbS)?
6th AA in beta chain - Glu switches out for Valine So negative for a nonpolar AA! Homozygous, but heterozygotes have milder sickling. Very short lifespan vs normal 120 days Hydrophobic nature makes it prone to polymerizing in vessels when deoxygenated Hb state.RBC's clump up and lead to intense pain due to ischemia, Anemia (duh), Stroke and death possible if not managed. No signs of HbS in womb since HbF is present. Heterozygotes for HbS is shown to be protective against Malaria
During an experiment, an investigator studies a toxin produced by Corynebacterium diphtheriae that inhibits protein synthesis. This inhibition is mediated via the post-translational modification of a protein. Which of the following best describes the nature of this post-translational modification? A. ADP ribosylation B. Ubiquination C. Glycosylation D. Phosphorylation E. Methylation
A. ADP ribosylation Answer A - This isn't something that you'll need to know for class, but it was on my NBME. Make sure you know what the general functions and structures of these others are tho! B - Degradation of proteins via proteosome, mainly misfolded or damaged
A healthy adult is placed on a diet that lacks tyrosine, but is otherwise balanced. As a result of this diet, nitrogen balance is most likely which of the following? A. Be achieved B. Become negative C. Become positive D. Progress from a negative state to equilibrium E. Progress from a positive state to equilibrium
A. Be achieved We can immediately eliminate D and E, as these are saying that were going from one state of nitrogen balance to equilibrium. To go from a negative state to equilibrium we would have to eat more protein, to go from a positive state to equilibrium, we would have to omit an essential amino acid or not eat enough
Dude comes in, bending his fingers vertically and stretching his skin. Diagnosis? A. Ehlers-Danlos syndrome B. Scurvy C. Marfan's syndrome D. Schizophrenia
Answer A - It's typically easy to diagnose EDS on exams. Remember stretchy skin, hypermobility in joints, & most dangerous, easily ruptured blood vessels. Also remember that this involves collagen. B - skkkkkuuuurrrryyy vit C deficiency - more on that next week in vitamins (high yield btw) C - defective fibrilin scaffold for elastin D - because he's insane???
In contrast to hemoglobin A, which of the following properties of hemoglobin F aids significantly in the delivery of oxygen across the placenta? A. Lower affinity for 2,3-bisphosphoglycerate B. Lower affinity for CO C. Lower cooperativity in binding D. Lower protoporphyrin affinity for iron
Answer A - Since HbF (fetal hemoglobin) does not have beta-subunits (2 alpha & 2 gamma subunits), it does not have the crevasse in which 2,3-BPG can fit. Thus, HbF has lower affinity to 2,3-BPG than HbA. This is the basis for fetal hemoglobin accepting oxygen from a mother's HbA.
Which residue on myoglobin helps stabilize the binding of O2 to Fe2+? A. Proximal His B. Distal His C. Proximal Glu D. Distal Glu
Answer B - The distal Histidine residue (His 64, E7) - this is the most important residue for binding O2. Mutations affecting proteins at this residue have detrimental effects. A - binds to the iron in the heme group of myoglobin (His 93, F8) C & D would have detrimental effects since Glu is -1.
An African-American male came into the hospital suffering from a painful crisis following strenuous exercise. His symptoms are likely due to: A. Oxidation of heme groups B. Hydrophobic interactions of deoxygenated Hb C. Hydrophobic interactions of oxygenated Hb D. Aggregation of gamma-tetramers
Answer B - This patient has sickle cell anemia. A point mutation leads to the switch of Glu (-1) to Va (+0), resulting in a hydrophobic AA on the outer surface of Beta-subunits. This attracts other hydrophobic patches on other hemoglobin and causes molecules to aggregate. This hydrophobic patch is on the outer surface of hemoglobin when it is in its deoxygenated form, which usually only occurs in times of painful crisis (factors shifting the curve right). A - Methemoglobin C - hydrophobic patch isn't on outer surface when Hb is bound to oxygen D - this is Hb barts (alpha thalassemia) - results in intrauterine death
In aging, wrinkles around eyes may be a result of: A.Increased extracellular cleavage of collagen B. Decreased collagen fibril production C. Mutation in alpha-antitrypsin D. Mutation in Chromosome 7 E. Mutation in chromosome 13
Answer B - Wrinkles are a result of decreased collagen fibril production as we age. This was a question on our exam last term. Answers D&E - Make sure you know these chromosome (7 - elastin gene: mutation = William's syndrome) (13 - fibrilin gene: mutation = Marfan's syndrome)
Alport syndrome is an X-linked disorder affecting which type of collagen? A. Type 1 B. Type 2 C. Type 3 D. Type 4 E. Type 5 F. Type 7
Answer C - Alport syndrome in Type 4, the main type of collagen in the basement membrane of cells. For this class, just know Type 1 & 4. You'll learn the others in histo: 1 - the most common, found in bones & sclera of eyes (Osteogenesis imperfect) 2 - main collagen in hyaline & articular cartilage 3 - Reticular fibers 4 - BM 5 - also found in bones (less than type 1) 7 - binds type 4 at junction of epidermis & dermis
A 3-year-old boy is admitted to the hospital because of an 18-month history of recurring fractures of the long bones. Physical examination shows bowing and deformities of the lower limbs. X-rays of be long bones show evidence of previous fractures and osteopenia. A biopsy specimen of skin shows unstable collagen, type 1. Further analysis shows a single point mutation in one of the genes encoding collagen, type I. This mutation most likely caused which of the following amino acid substitutions in this patient? A. Ala -> Asp B. Glu -> Pro C. Gly -> Leu D. Tyr -> Trp E. Pro -> Ala
Answer C - The disease here is osteogenesis imperfecta. Key clinical features include: bowing of legs, easily fractured "brittle bones," bruising and frequent injuries (often thought as child abuse), and blue sclera. Make sure to know the formula for type 1 collagen (gly-x-y-)n (x = often Pro, y = hydroxyproline/hydroxylysine) and that for Elastin (-Gly-(Ala/Val)-x-)n. Elastin typically has no hydoxylysl, little hydroproyl, but also has a lot of Pro. Glycine has a small side chain allowing for the formation of the triple helix of type 1 collagen. It is typically 1/3 of the AA residues in collagen. Leucine is a bulk AA. In a collagen triple helix, this creates steric hindrance, thus disrupting the structure of collagen.
A patient comes into your clinic with shortness of breath, cyanosis, and hypoxia. You decide methylene blue treatment will provide the best prognosis. Methylene blue is which of the following? A. An anticoagulant B. An oxidizing agent C. A reducing agent D. A sulfonamide
Answer C - This patient has Chocolate cyanosis - increased Methemoglobin in the blood. Methemoglobin is oxidized hemoglobin, containing iron in the ferric state (Fe3+). When hemoglobin is oxidized, it cannot bind oxygen. Methylene blue is used in treatment to reduce the hemoglobin from Fe3+ to Fe2+, and is thus a reducing agent. (Methemoglobin = chocolate-colored blood) Note: Sulfonamides given to infants can cause release of unconjugated bilirubin from albumin and may lead to kernicterus as the unconjugated bilirubin enters the brain.
Kayser-Fleischer rings are deposits of copper in the cornea due to defective transport. This can identify if a patient has: A. Menke's syndrome B. Marfan's syndrome C. Wilson's disease D. William's syndrome
Answer C - Wilson's disease. Also remember the gene ATP7B. Menke's syndrome - defective transmembrane protein (Copper) - Gene ATP7A Marfan's syndrome - defective fibrilin - FBN 1 gene (chromosome 15) William's syndrome - defective elastin - large deletion (chromosome 7)
Which of the following vitamins act as coenzyme for protein carboxylase enzyme and helps in the activation of clotting factors II, VII, IX and X by gamma carboxylation there by helps in the thrombus formation? A. Vitamin A B. Vitamin B7 C. Vitamin K D. Vitamin E E. Vitamin C
Answer C - this is about the only exception you'll see when "carboxylation" doesnt involve B7. Gamma Carboxylation at Glu residues activates blood clotting factors with the help of vitamin K (special type of post-translational modification)
A long-time smoker comes into your clinic with difficulty breathing. Physical examination shows reduced lung capacity. Genetic analysis determine the patient was heterozygous for a transition mutation of α-antiproteinase. Which of following is the underlying basis for these clinical findings? A. The mutation involves Lys -> Val B. The mutant protein cannot cleave collagen C. The mutant protein cannot cleave elastin D. Oxidation of a Met residue E. Elastin is unable to crosslink
Answer D - In smokers, smoking causes a oxidation of an important Met residue involved with the binding of α-antiproteinase to elastase. As a serine protease inhibitor, α-antiproteinase binds & inhibits elastase, preventing it from breaking down elastin. If α-antiproteinase cannot bind elastase, elastase is free to cleave elastin, making the lungs more inelastic and reducing their lung capacity. This leads to emphysema. A - the mutation is Lys->Glu. Make sure you know this! C - it prevents elastase from cleaving elastin
Working as a doctor without borders in Uganda, you meet a young patient suffering from SOB. Physical examination reveals swollen ankles, fluid in the abdomen, and heart murmurs. A deficiency of which vitamin may have cause this dilated cardiomyopathy? A. Ascorbic acid B. Retinol C. Riboflavin D. Thiamine E. Folic acid
Answer D - Uganda is a developing country, were Beri Beri is common due to the lack of Vitamin B1. Biventricular dilation of the heart results from thiamine deficiency. Beri beri is characterized by cardiovascular problems.
A chronic alcoholic develops severe memory loss with marked confabulation. Deficiency of which of the following vitamins would be most likely to contribute to the neurologic damage underlying these symptoms? A. Folic acid B. Niacin C. Riboflavin D. Thiamine E. Vitamin B12
Answer D - this is a classic example of Wernicke-Korsakoff syndrome from a thiamine deficiency. Chronic alcoholism impairs thiamine absorption, leading to neurological symptoms common to alcoholics.
In which cellular compartment is procollagen cleaved? A. Rough ER B. Golgi Apparatus C. Nucleus D. Mitochondria E. Extracellular space
Answer E - Procollagen is cleaved by procollagen peptidase into collagen in the extracellular space, where procollagen is secreted. A - after translation, Pro & Lys residues on pro-collagen are hydroxylated in the RER by lysl/prolyl hydroxlyase (a process which requires vitamin C). As they are hydroxylated, they form a triple helix structure (NOTE: this triple helix is different than an alpha helix, which is why it has proline) B - Following hydroxylation, the procollagen molecule is sent to the GA where it is glycosylated at Lys residues. Following this, procollagen is secreted in to the ECM. C - nucleus is only involved in forming its mRNA D - not involved
Which of the following is the only water-soluble vitamin that is stored in liver? A. Vit C B. B1 C. B2 D. B5 E. B9 F. B12
Answer F - Vitamin B12 (Cobalamin) is the only stored water soluble vitamin and is also only found in animal products. This vitamin is essential for blood cell formation (hematopoiesis). B12 deficiency is often masked by B9 deficiency, but both can result in megaloblastic anemia (RBCs are to big, prone to lysis)
After hydrolysis of the peptide bonds in a short polypeptide, the following amino acid was identified in a solution. Acid-base titration was performed, and it was determined that the amino acid has three distinct pKA values: 2.2, 9.2 and 10.7. At physiological pH, which of the following is the most likely net charge of the pictured amino acid A.) +2 B.) +1 C.) 0 D.) -1 E.) -2
B) +1 So this question depends on your knowledge of pKA's. You don't really need the image to help you solve this question, because it tells you the amino acid. Since there are 3 pKA's, that means the amino acid has an acidic or basic side chain. In looking at the three values, you can see that two of them are very
An insoluble form of a prion protein accumulates in the brains of patients who have Creutzfeldt-Jakob disease. Conversion of the normal soluble form of the prion protein to the pathologic insoluble form is thought to involve conversion of a-helices to b-pleated sheets. This transition requires breaking and reformation the following? A. Disulfide bonds B. Hydrogen bonds C. Peptide bonds D. Salt bridges E. Zinc fingers
B. Hydrogen Bonds
DNA is located inside the nucleus and is wrapped tightly around proteins called histones. These proteins have abundant lysine residues. Which change to this amino acid would affect DNA binding the most? A.) Leucine B.) Valine C.) Arginine D.) Glutamate E.) Cysteine F.) Phenylalanine
D) Glutamate A first glance this question may look impossible. But most questions involving amino acids simply have to do with the properties of those amino acids, whether there polar, nonpolar or charged DNA is negatively charged, so you have to know that. It binds to histones so well because histones are covered in lysine residues. Lysine has a positive charge, and the negatively charged DNA is attracted to lysine. So we are essentially looking for an amino acid that has a charge that will not attract a negative charge. If we look at the answer choices we can eliminate a few right away. Leucine, valine, phenylalanine, and cysteine all have no charge. But let's just look at leucine in valine. These are both nonpolar meaning they are both wrong, because they're in the same class so one can't be writes first the other. And first glance, a nonpolar amino acid could work. Because a negative charge DNA couldn't bind to it. However, since there is to nonpolar answers it can't be both. Plus the question is asking which one affected the most, and the negatively charged wood affected the most because it would repel it Arginine is positively charged just like lysine, so this wouldn't affect DNA-binding at all Assisting in phenylalanine also do not have a charge (but they are polar, but that doesn't affect the question) Glutamate is the only one with a negative charge, meaning and negatively charged DNA molecule would be repelled
During periods of drought, the leaves of desert trees often become a dietary staple for certain populations. Which of the following amino acids, present in sufficient quantity in the leaves, satisfies an essential nutritional requirement? A. Alanine B. Aspartate C. Glutamate D. Methionine E. Serine
D. Methionine Answer D - Met is the only essential AA listed. Make sure you know these, they seem to be high yield. A good way to remember essential AAs is negatively charged AAs (Asp/Asn, Glu/Gln), Met, serine, and alanine.
What is Met-Hb Chocolate Cyanosis?
Iron becomes oxidized and losses an electron becoming Fe3+. Oxygen doesn't bind in this form. Enzyme NADH methemoglobin reductase fixes the problem. Can be identified be dark brown blood and treated by methylene blue.
When is the best time to view the chromosomes during mitosis?
Metaphase as they are lined up on the metaphase plate
Answer A - You should know the amino acids involved in the mutations of HbC & HbS. For HbC, the mutation causes a Glu residue to be replaced with Lys, making the molecule more positive. In HbS, a Glu residue is replaced with a Val residue. Since Glu is a negatively charged AA, both HbC & HbS are more positively charged than HbA. Thus, HbC (contains Lys, +1) migrate closer to the positively charged anode than HbS (contains Val, +0), and HbS migrates closer to it than HbA (contains original Glu, -1). Like chromatography, anodes attract anions. Note: Because HbC has a mutation involving a charged AA to a different charged AA, its properties are slightly retained. Whereas HbS's mutation involves a switch from a charged AA t
One form of mild, hemolytic anemia is HbC. HbC results from a transition mutation of GAG -> AAG. The following gel shows hemoglobin separated by charge, with the positively-charged anode at the bottom of the gel. X marks HbA. Which of the following represents HbC?
How do you calculate the ph of Histidine?
Since Histidine is Alkaline in nature, the pKA of 6.00 + 9.16 should be divided by 2 to = 7.58
What is the protein folding funnel model?
The protein folding funnel model is model that states that unfolded proteins begin at a high energy state and undergo hydrophobic interactions, hydrogen bonding, Van der Whals interactions and electrostatic interactions to continuously fold into a lower energy state. With the help of chaperone proteins, which guide protein folding, the protein can reach its lowest every state called a native protein. Improper folding leads to high energy aggregates and amyloid fibrils which are ether guided by chaperones to a lower energy state or eliminated by the Ub pathway
What is the R state of hemoglobin?
The relaxed state in which O2 affinity is high
G2 phase
The second growth phase of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs. This is a checkpoint for DNA replication.
What is the T state of hemoglobin?
The tense state in which O2 affinity is low
secondary structure of protein
The way in which the chain of amino acids of the polypeptides of a protein is folded due to hydrogen bonding. Alpha-Helix and Beta-Sheets
The effect of 2,3-BPG on oxygen binding
Transfused blood destroys the 2,3-BPG. Hb in the blood will have a high affinity for O2. Treatment of Inosine will help RBCs make 2,3-BPG
Which aromatic amino acid is responsible for melanin, plays a role in dopamine production and is used in glycogen synthesis?
Tyrosine
What is western plotting?
Used for plotting proteins
Does the peptide bind have double bond character?
Yes, at the C-termnis
The Bohr Effect
a decrease in the amount of oxygen associated with hemoglobin and other respiratory compounds in response to a lowered blood pH resulting from an increased concentration of carbon dioxide in the blood.
Chromotography
a process which separates the parts of a solution with special paper and a solvent.
gel filtration chromatography
a type of column chromatography that separates proteins based on their size using size-exclusion beads; also called size-exclusion chromatography Larger proteins elute first followed by small proteins
denaturing proteins
heat or low ph denatures proteins - protein doesn't function; changes structure;
Prophase I (Meiosis)
homologous chromosomes pair up and form tetrads, crossing over occurs
paper chromatography
method of separating a mixture of different colours. The liquid soaks through the paper and carries the mixture with it. Some substances are carried faster than others so the substances are separated along the paper. The more polar the substance the higher it travels on the paper.
quaternary structure of a protein
protein structure is a protein consisting of more than one folded amino acid chain. Hemoglobin is an example.
tertiary structure of protein
protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure
native gel electrophoresis
separates proteins on the basis of their net charge at the pH of the electrophoresis buffer. More negative will move down the gel towards the positive end and the more positive will remain higher in the gel
primary structure of protein
the amino acid sequence of the polypeptide chain
affinity chromatography
uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest The protein of interest becomes stuck in the matrix
