BB WRONG Flashcards
review all amino acids
Secondary structure
alpha helical & Beta sheets
hydrogen bonds
Kd
- dissociation constant, measures the dissociation of the substrate from the ES complex.
- Binding affinity is typically measured and reported by the equilibrium dissociation constant
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MOST EFFECTIVE TO BIND::LOWEST Kd
- larger Kd, the less affinity the enzyme has for the substrate
- Km is a measure of affinity, and is the concentration of substrate that reaches 1/2 Vmax.
What should be assumed when said “amino acid cleaved”
- hydrolytic cleavage—-> proteases
Ribonuclease
is a type of nuclease that catalyzes the degradation of RNA into smaller components
Entropy penalty
- amino acid substituion from Leu to Thr at surface-exposed sites will result in DECREASED ENTROPY PENALTY
- Because changing a surface-exposed hydrophobic residue for a more hydrophilic residue elimates the entropic penalty associated with ordered water molecules around hydrophobic groups
Introns
- occurs posttranscriptional
- DNA to premRNA is transcription
- premRNA to mRNA is posttranscriptional
mRNA processing in prokaryotes
- mRNA processing doesn’t occur in prokaryotes
- becuase transcription in prokaryotes occurs in cytoplasm, ribosomes are able to bind & begin translation even before transcription is complete, prokaryotic mRNA requires NO ADDITIONAL processing after transcription
PCR primer
- CG
- suitable primer have a high CG content and have a G or C base pairs at 5’ to 3’ ends
Endothelium Mutation
Inheritance patterns: AUTOSOMAL
recessive disorders
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autosomal recessive inheritance: both copies of the gene in each cell have mutations.
- The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but they typically do not show signs and symptoms of the condition
- normal son cannot have hemophillic (recesssive) mother & hemophilic daughter (recessive) cannot have normal father
- autosomal dominant inheritance: is a pattern of inheritance characteristic of some genetic diseases. “Autosomal” means that the gene in question is located on one of the numbered, or non-sex, chromosomes. “Dominant” means that a single copy of the disease-associated mutation is enough to cause the disease.
in the hydrolysis reaction for GTP/GDP which is active/inactive?
active GTP——> inactive GDP
HA–><– H+ + A-
when HA dissociates fully in blood, what happens?
Due to La Chatlier’s principle, the equilibrium will favor products when the conc of the products is kept low, so here it will shift to the right
if we inc proinsulin, what happens to insulin and blood glucose levels?
increase in proinsulin—->increase insulin—>decrease blood glucose
Metabolic rate
- will enable one to determine how long the stored energy reserves will last
- an organism that has low metabolic rate & thus a larger-lasting energy reserves will be best suited to withstand periods of long term nutrient deprivation
Absence of O2 will result in what with Acetyl CoA
- low amount of acetyl CoA is produced in the absence of O2, because krebs produces acetyl CoA in O2
Fermentation—>lactic acid—->no O2—–>???
Fermentation—>lactic acid—-> O2—>???
- NO O2, thus lactic acid stays in cytoplasm
- with O2, lactic acid goes to acetyl CoA
Protein transport
Retrograde protein transport
- protein translation occurs in ER
- protein then transported to golgi for post translational modification, processing, & packaging for proper localization
- retrograde transport would reverse the motion and return protein to the ER
Individual cells making up a tissue different from single-celled organisms such as paracelium in that only the latter:
- latter (paracelium) are capable of extended independent life
- tissue cells are dvided by mitosis
- tissue cells contain subcellular organellles
- tissue cells can metabolize nutient molecules
- tissue cells are not capable of extended life
when graph gives *, know it means significance
pay attetnion to those
Covalent & noncovalent bonds
peptides are covalent bonds
Adaptive Immune System
Antigens & antibodies
- immune system recognizes the mouse antibody as a foreign antigen & generate an immune response towards it, which may include a mild to severe allergic response
- the immune response will generate antibodies against the mouse, limiting its usefulness as an antibody treatment
Bicarb Buffer System
veins & arteries CO2 concentration
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veins= INC CO2
- Cl- will be higher in veins because HCO3- is higher in veins
- arteries= DEC CO2
Surface area & RBC
max exposure of each RBC to diffusing gases will aid respiration by RBC by being in a single line
Q 28: 1A: Skill 4: passage based
given this graph: what can we say about AcTubK40
- look at the X & Y axis, we see that the protein acetylation level (fold) is constant, it stays at 1.
- BHOB does not change the AcTubK40 acetylation level, but it does change the other 2
- thus we can infer that BHOB is specific to the other two, thus it is not a general deacytalse inhibitor
- Answer A is wrong: becuase the data/passage gave one potential non-histone target (tubulin)
- Answer C is wrong: becuase BOHB was adminstered outside the cells (exogenous), which means it must diffuse through both the plasma membrane & the cytoplasm to get into the nucleus & affect HDACs; therefore it is unlikely that BOHB is only in the nucleus
Q47: 1A: skill 2: discrete
rate of typical enzymatic reaction is increased how?
pay attention to the wording of the question, TYPICAL!!
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Answer: increase in temperature from 20C to 37C
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increasing temperature increases rate of reaction because more molecules possess enough energy to overcome the energetic barrier of a reaction (activation energy) at a higher temperature
- for the sake of kinetics, unless explicity says in the passage, the only 2 things that can effect the rate of the reaction are temperature & enzymes.
- Optimum pH value varies greatly from one enzyme to another, the optimum temp for enzymes is normally 37C
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increasing temperature increases rate of reaction because more molecules possess enough energy to overcome the energetic barrier of a reaction (activation energy) at a higher temperature
_____________________________________
what else increases reaction rate?
- rate of reaction increases with inc substrate conc-think MM curve
- increasing pH may or may not increase the reaction rate-becuase we don’t know if increasing the pH will denature the enzyme or not
- decreasing Ea will inc reaction rate
Q41: 1B: skill 1: passage based (go over it)
protein translation
Assuming that protein synthesis was under way when the radioactive amino acids were added, which of the following best describes how the radioactivity was distributed in one of the first molecules of Protein X that was completely translated?
- becuase the stem says that translation (protein sysnthesis) was underway, we can assume that the first half of the protein will contain normall AA’s.
- per passage: At time = 0 s, radiolabeled amino acids were added to a flask containing S. cerevisiae in a growth medium. After 50 s, a large excess of nonradioactive amino acids was added.
- then the radioactive ones are added, which will be incorprated on the C-terminus end of the protein as it finishes being translated (aa are incorprated from the amino to the carboxy terminus); therefore they will only be found on one side of the protein
- Thus the protein should look like:
NH2 END- NONRADIOACTIVE (Pre 0 seconds) l Radioactive (0-50 seconds) l Nonradioactive (50-X seconds, assume small) l Radioactive amino acids (50-300 seconds) - COOH END
Q6: 1 C: Skill 2
Autosomal dominant & autosomal recessive
https: //ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns
https: //blog.blueprintprep.com/mcat/mcat-genetics-a-quick-guide-to-recognizing-modes-of-inheritance/
- the inheritance of HPRCC is autosomal dominant
- we see that the offspring show a 3:1 inheritance pattern
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there are also no skipped generations-which is a sign of dominant trait
- because the allele must be inherited in a autosomal dominant pattern in order for individuals II-1 and II-2 to produce both affected and unaffected offspring.
- The inheritance pattern for the offspring of these individuals is consistent with autosomal dominant if the parents are heterozygous. The rest of the pedigree is consistent with this mode of inheritance as well.
- In addition, the offspring of individuals II-1 and II-2 rule out autosomal recessive (will show unaffected offspring), X-linked recessive, and Y-linked (if disease was a y-linked-only males would have this trait)
Q51: 3A: skill 2: passage based
A drug that inhibits the activity of which of the following enzymes would be most likely to relieve depression in some people, assuming the chemical reactions in Figure 1 are irreversible?
- Answer: monoamine oxidase A
- because based on the data in Figure 1, monoamine oxidase A is involved in oxidation and degradation of serotonin. Therefore, a drug that inhibits the activity of monoamine oxidase A would be most likely to relieve depression.
- If you block the enzyme that degrades serotonin = more serotonin = less depressed
Fun fact but Monoamine Oxidase Inhibitors (MAOIs) are actually a class of anti-depressant medication
cyclobutane pyrimidine dimer image
- image that displays a dimer of two pyrimidine residues.
- silly mistake, I choose the 2 purines.
- Dimer indicates that it is a molecular complex consisting of two identical parts (unless specifically mentioned as a heterodimer). Also remember that purines consist of 2 rings and pyrimidines consist of 1 ring.
what does fluoresece do?
- it exposes the amino acids
- in the presence of DPC, fluorescence of protein X increases greatly. this indicates that is has adopted a conformation that exposes hydrophobic residues on its surface; The graph shows measurement of ANS flouresecence and passage explains that ANS “exhibits increased flourescence upon binding hydrohobic surface residues of protein” so in order to observe increased fluorescence, the addition of DPC must do something the makes the binding of ANS to hydrophobic residues easier, such as exposing them.
phosporylation makes aa more polar
variable region of antibody
regions 1 and 3 correspond to the variable portion of the light and heavy chains, respectively, of an antibody. The variable region of an antibody will enable recognition of a particular antigen, such as HER2, which typically has elevated expression in breast cancer tumors.
