AAMC BBCF Flashcards
what steps of muscle contraction require ATP
Dissociation of the myosin head from the actin filament requires the binding of ATP
The conformational changes that move actin and myosin relative to one another require that ATP be hydrolyzed, for these changes occur upon release of the products of hydrolysis (ADP and Pi) by the myosin head
what is the electron acceptor in the production of lactate
In this process, NADH reduces pyruvate to produce lactate. Therefore, pyruvate serves as the electron acceptor in production of lactate.
define the following
- competitive inhibition
- noncompetitive inhibition
- uncompetitive inhibition
competitive binds directly to the active site that a substrate would normally occupy
noncompetitive binds to an allosteric site that changes the shape of the active site such that a substrate cannot bind OR to the enzyme-substrate complex that prevents any catalysis from happening
– includes mixed inhibition
uncompetitive binds to an allosteric site on the ES complex that prevents any catalysis from happening
Km and Vmax changes + graph
- competitive inhibition
- noncompetitive inhibition
- uncompetitive inhibition
- mixed inhibition
competitive inhibitor = lower x-int (higher Km) and same y-int (Vmax unchanged)
noncomp inhibitor=same x-int (Km unchanged) and higher y-int (lower Vmax)
uncomp inhibitor = higher x-int (lower Km) and higher y-int (lower Vmax)
mixed inhibitor=lower x-int (higher Km) and higher y-int (lower Vmax)
vasoconstriction / dilation and microfilament polymerization
Vasoconstriction is marked by polymerization of actin (getting longer); vasodilation is the depolymerization of actin (getting shorter).
epimer vs enatiomer
Epimers refer to molecules with several stereocenters where only ONE configuration is different. For example D-glucose and D-galactose are the exact same except for they have an opposite configuration at carbon 4, so they are 4-epimers.
Enatiomers refer to molecules that have one or more stereocenters with opposite absolute configurations (R/S) at each one.
epimer vs enatiomer vs diastereomer
Epimers refer to molecules with several stereocenters where only ONE configuration is different.
Enatiomers refer to molecules that have all of their stereocenters inverted
Diastereomers refer to molecules that have more than one BUT NOT ALL of their stereocenters inverted
alpha beta designation
α versus β designation distinguishes between molecules with multiple chiral centers, but differ only in the configuration of the site known as the anomeric carbon atom.
epimers!
southern plot
uses a restriction digest to differentiate between mutant and wild-type alleles
n order for a Southern blot to be useful, the mutation should either create or eliminate a restriction site, most of which are palindromes and 4 to 6 base pairs long.
– A Palindromic sequence, where a restriction enzyme cuts, has the same 4-6 nucleotide long sequence in the 5’-3’ direction on both strands
eg. For example. 5’-AAGCTT-3’ IS a palindromic sequence because the complimentary strand 5’-3’ will be identical. GOOD!
BUT 5’-AGCCGA-3’ may look like a palindrome (and is of the type like ‘racecar’ or ‘noon’), but this clearly does not qualify in the Biological/Genetic sense as the complimentary strand would not be identical. BAD!
SNOW DROP mnemonic
Southern=DNA
Northern=RNA
O=O
Western=Protein
average molecular weight of an amino acid
how much would a monomer of 288 AA’s weigh in a tetramer?
110 Da
monomer is composed of 288 amino acids, which will have an approximate molecular weight of 32 kDa»_space; tetramer (four monomers) will thus have an approx molecular weight of 128 kDa
hill coefficient
measures cooperativity
n>1 = cooperativity
n=1 no cooperativity
n<1 = negative cooperativity
what does a small Kd mean
how do you calculate catalytic efficiency
Small Kd = high affinity because smaller concentration of substrate required to saturate 50% of the enzyme available
Kcat/ Km = catalytic efficiency
how are isoforms produced
Different protein isoforms are synthesized from the same gene through alternative splicing, during which sections of the full transcript (both introns and exons) are spliced.
Different combinations of exons can produce different protein isoforms.
glands are what cell
EPITHELIAL
peptide hormones
hydrophilic and soluble in blood
Hormones that must bind transport proteins are steroid proteins, which are lipophilic.
slope of lineweaver-burk plot
Km / Vmax
nuclear factor
nuclear factors are the only elements that vary in different cells and therefore can confer both temporal and spatial regulation of their target genes
glycogenolysis vs gluconeogenesis
glycogenolysis is catabolic vs. gluconeogenesis which is anabolic
glycogenolysis occurs in different tissues that store glycogen (ESPECIALLY muscle tissues, but unlike the liver, they use the released glucose for themselves energy-wise and don’t release any to the bloodstream), but gluconeogenesis occurs predominantly in the liver and, to a lesser extent, in the kidneys
glycogenesis
formation of glycogen from glucose using glycogen synthase
reversed by glyconeolysis
gluconeogenesis
process of synthesizing glucose from non-carbohydrate sources (eg pyruvic acid)
glycogenolysis
glycogen stored in the liver and muscles is broken down into energy
activated by glucagon and epinephrine»_space; stimulates glycogen phosphorylase to convert glucose 1 phospahte into glucose 6 phosphate
PFK opposite
phosphofructokinase - Glycolysis
– driven when there is too much AMP and when insulin drives the production of Fruc-2-6-bisphate, which also activates PFK
Opposite Fru-1-6-BisPhase (Gluconeogenisis)
– driven by ATP but regulated by AMP and Fru-2,6,-bisphosphate
which enzyme is used both in gluconeogenesis and glyconeolysis
glucose 6 phosphatase catalyzes the final step of both
how to determine the efficiency of an enzyme
[E] = kcat / Km
or Vmax = Kcat * [E]
what is involved in cDNA cloning
DNA polymerase (in DNA amplification), DNA ligase (in ligation of the cDNA to DNA vector) and reverse transcriptase (in reverse transcription of RNA to cDNA) are used during cDNA cloning,
RNA polymerase is not used in cDNA cloning.
what are the starting materials in gluconeogenesis?
lactate, oxaloacetate, and α-ketoglutarate
g protein pathway: phosphodiesterase
- An appropriate molecule binds to a G-protein receptor.
- The receptor causes the release of the alpha subunit of a G-Protein.
- The alpha subunit activates adenylyl cyclase, which generates cAMP.
- cAMP phosphorylates and thereby activates Kinase A, which goes on to phosphorylate and activate other proteins.
- Phosphodiesterase degrades cAMP to stop the signal (and biological pathway) originally started by the molecule attaching to the G-Protein Receptor
g protein pathway: phospholipase
- Ligand binds to Gq receptor.
- Alpha subunit of the heterotrimeric G protein released and is the active form of the G protein.
- Activates PLC, which converts PIP2 to DAG and IP3.
- IP3 is the second messenger (like cAMP in the other pathway) and it causes the release of Ca2+ from the endoplasmic reticulum.
- This increases the intracellular concentration of Ca2+.
- The increased levels of Ca2+ along with DAG (produced in step 3) activate Protein Kinase C.
- Protein Kinase C phosphorylates and activates other proteins.
what enzyme catalyzes what step of glycogenolysis
Glycogen phosphorylase is the enzyme that catalyzes the rate-limiting step in glycogen breakdown
how are glucose polymers formed
the glucose polymer in liver (glycogen) is formed by glycosidic bonds between glucose molecules through α(1→4) linkage linearly and α(1→6) linkage at branch point
what compounds are considered gluconeogenic precursor or substrate
lactate, oxaloacetate, glycerol
what happens what something affects the gradient of the ETC
The electron transport chain uses the free energy from redox reactions to pump protons from mitochondrial matrix to the intermembrane space thereby generating an electrochemical gradient across the inner mitochondrial membrane.
Therefore any event that causes the dissipation of the electrochemical gradient across the inner mitochondrial membrane will result in decreased level of protons in mitochondrial intermembrane space.
for any given gene, the nucleotide sequence …
for any given gene, the nucleotide sequence of both the coding strand and the mRNA are complementary to the sequence of the template strand
Chylomicrons and VLDLs
Both contain apolipoproteins and primarily transport triacylglycerol
The only major difference between them is the tissue of origin. Chylomicrons transport dietary triacylglycerol and originate in the small intestine, while VLDLs transport newly synthesized triacylglycerol and originate in the liver.
micelles and chylomicrons
Micelles are formed by the hydrophobic effect where the tails of the phospholipids aggregate to the center and the hydrophilic heads protrude outward to interact with water molecules. Chylomicrons are lipoproteins that transport lipids in the form of triacyglycerols (glycerol esterified to 3 fatty acids) to body tissues.
The main difference in structure is that micelles are just made up of phospholipids whereas chylomicrons are made up of triacylglycerols and phospholipids.
What role does peptidyl transferase play in protein synthesis?
enzyme that catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the growing polypeptide chain in the P site
