AAMC BBCF

Question 1

what steps of muscle contraction require ATP

Answer 1

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

Question 2

what is the electron acceptor in the production of lactate

Answer 2

In this process, NADH reduces pyruvate to produce lactate. Therefore, pyruvate serves as the electron acceptor in production of lactate.

Question 3

define the following

• competitive inhibition
• noncompetitive inhibition
• uncompetitive inhibition

Answer 3

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

Question 4

Km and Vmax changes + graph

• competitive inhibition
• noncompetitive inhibition
• uncompetitive inhibition
• mixed inhibition

Answer 4

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)

Question 5

vasoconstriction / dilation and microfilament polymerization

Answer 5

Vasoconstriction is marked by polymerization of actin (getting longer); vasodilation is the depolymerization of actin (getting shorter).

Question 6

epimer vs enatiomer

Answer 6

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.

Question 7

epimer vs enatiomer vs diastereomer

Answer 7

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

Question 8

alpha beta designation

Answer 8

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!

Question 9

southern plot

Answer 9

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!

Question 10

SNOW DROP mnemonic

Answer 10

Southern=DNA
Northern=RNA
O=O
Western=Protein

Question 11

average molecular weight of an amino acid

how much would a monomer of 288 AA’s weigh in a tetramer?

Answer 11

110 Da

monomer is composed of 288 amino acids, which will have an approximate molecular weight of 32 kDa&raquo_space; tetramer (four monomers) will thus have an approx molecular weight of 128 kDa

Question 12

hill coefficient

Answer 12

measures cooperativity

n>1 = cooperativity

n=1 no cooperativity

n<1 = negative cooperativity

Question 13

what does a small Kd mean

how do you calculate catalytic efficiency

Answer 13

Small Kd = high affinity because smaller concentration of substrate required to saturate 50% of the enzyme available

Kcat/ Km = catalytic efficiency

Question 14

how are isoforms produced

Answer 14

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.

Question 15

glands are what cell

Answer 15

EPITHELIAL

Question 16

peptide hormones

Answer 16

hydrophilic and soluble in blood

Hormones that must bind transport proteins are steroid proteins, which are lipophilic.

Question 17

slope of lineweaver-burk plot

Answer 17

Km / Vmax

Question 18

nuclear factor

Answer 18

nuclear factors are the only elements that vary in different cells and therefore can confer both temporal and spatial regulation of their target genes

Question 19

glycogenolysis vs gluconeogenesis

Answer 19

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

Question 20

glycogenesis

Answer 20

formation of glycogen from glucose using glycogen synthase

reversed by glyconeolysis

Question 21

gluconeogenesis

Answer 21

process of synthesizing glucose from non-carbohydrate sources (eg pyruvic acid)

Question 22

glycogenolysis

Answer 22

glycogen stored in the liver and muscles is broken down into energy

activated by glucagon and epinephrine&raquo_space; stimulates glycogen phosphorylase to convert glucose 1 phospahte into glucose 6 phosphate

Question 23

PFK opposite

Answer 23

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

Question 24

which enzyme is used both in gluconeogenesis and glyconeolysis

Answer 24

glucose 6 phosphatase catalyzes the final step of both

Question 25

how to determine the efficiency of an enzyme

Answer 25

[E] = kcat / Km

or Vmax = Kcat * [E]

Question 26

what is involved in cDNA cloning

Answer 26

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.

Question 27

what are the starting materials in gluconeogenesis?

Answer 27

lactate, oxaloacetate, and α-ketoglutarate

Question 28

g protein pathway: phosphodiesterase

Answer 28

1. An appropriate molecule binds to a G-protein receptor.
2. The receptor causes the release of the alpha subunit of a G-Protein.
3. The alpha subunit activates adenylyl cyclase, which generates cAMP.
4. cAMP phosphorylates and thereby activates Kinase A, which goes on to phosphorylate and activate other proteins.
5. Phosphodiesterase degrades cAMP to stop the signal (and biological pathway) originally started by the molecule attaching to the G-Protein Receptor

Question 29

g protein pathway: phospholipase

Answer 29

1. Ligand binds to Gq receptor.
2. Alpha subunit of the heterotrimeric G protein released and is the active form of the G protein.
3. Activates PLC, which converts PIP2 to DAG and IP3.
4. IP3 is the second messenger (like cAMP in the other pathway) and it causes the release of Ca2+ from the endoplasmic reticulum.
5. This increases the intracellular concentration of Ca2+.
6. The increased levels of Ca2+ along with DAG (produced in step 3) activate Protein Kinase C.
7. Protein Kinase C phosphorylates and activates other proteins.

Question 30

what enzyme catalyzes what step of glycogenolysis

Answer 30

Glycogen phosphorylase is the enzyme that catalyzes the rate-limiting step in glycogen breakdown

Question 31

how are glucose polymers formed

Answer 31

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

Question 32

what compounds are considered gluconeogenic precursor or substrate

Answer 32

lactate, oxaloacetate, glycerol

Question 33

what happens what something affects the gradient of the ETC

Answer 33

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.

Question 34

for any given gene, the nucleotide sequence …

Answer 34

for any given gene, the nucleotide sequence of both the coding strand and the mRNA are complementary to the sequence of the template strand

Question 35

Chylomicrons and VLDLs

Answer 35

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.

Question 36

micelles and chylomicrons

Answer 36

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.

Question 37

What role does peptidyl transferase play in protein synthesis?

Answer 37

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