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BCMB > UNIT 1 > Flashcards

UNIT 1 Flashcards

1
Q

Describe why water is such a great solvent of ionic substances and polar molecules.

A

polarity + uneven distribution of electrons

polar molecules attach to water instead of eachother
ionic substances dissociate into individual ions

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2
Q

What is the purpose of hydrogen bonding in water?

A

Produces a highly ordered and open structure

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3
Q

Hydrogen bonds are formed between:

A

water and other molecules

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4
Q

Water is said to be polar but uncharged. How is it possible?

A

The electrons in a water molecule are unevenly distributed. This results in oxygen holding a partial negative charge and the hydrogen holding a partial positive charge. This makes the bonds polar, but neutral as the charges cancel out.

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5
Q

What type of non-covalent interaction occurs between different water molecules?

A

hydrogen bonding

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6
Q

Could hydrogen bonding occur between two benzene molecules? Why or why not?

A

Hydrogen bonding cannot occur between two benzene molecules because they are nonpolar, hydrophobic molecules. They are not capable of chemical reactions with water.

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7
Q

Do any non-covalent interactions occur between water molecules and benzenes?

A

No, because benzene is a nonpolar, hydrophobic molecule. They hydrophobic effect will spontaneously occur.

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8
Q

Why do benzene molecules coalesce into a single larger one?

A

The association of benzene molecules releases some ordered water molecules around the separated benzenes, therefore INCREASING THE ENTROPY OF THE SYSTEM.

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9
Q

Define entropy

A

the degree of disorder in a system

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10
Q

2nd Law of Thermodynamics

In a spontaneous process, what happens to the total entropy of a system?

A

It increases (delta S is positive)

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11
Q

What is the equation for Gibbs Free Energy change?

A

∆G = ∆H - T∆S

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12
Q

What is the sign of ∆G for a spontaneous reaction?

A

Negative (∆G<0)

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13
Q

In what type of cells, and in what subcellular location, is hemoglobin normally found?

A

in the cytoplasm of red blood cells

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14
Q

What is the biological function of hemoglobin?

A

Hemoglobin is responsible for giving red blood cells their color. It transports oxygen and releases oxygen where necessary.

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15
Q

What type of amino acids fill the interior of the molecule?

A

nonpolar amino acids (hydrophobic)

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16
Q

Looking at the surface of hemoglobin, what type of amino acids predominate?

A

Charged, polar amino acids (hydrophilic) predominate in addition to nonpolar amino acids that make it water soluble.

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17
Q

What drives the hydrophobic effect?

A

An increase in entropy of the system

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18
Q

Based on Coulomb’s Law, what is the most important commonality among the non-covalent interactions?

A

the attraction of opposite charges

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19
Q

What must happen energetically in order to break non-covalent interactions?

A

the energy in the system must be greater than the non-covalent interactions

20
Q

What happens energetically when the non-covalent interactions form in the folded protein?

A

energy is released as the bonds form

21
Q

For protein folding, what is the sign of ∆H? ∆S? ∆G?

A

∆H: negative
∆S: positive
∆G: negative

22
Q

Is the ΔG positive or negative for micelle (and membrane) formation? Explain or show your work.

A

Negative bc micelle formation is also a spontaneous process.

23
Q

Why is protein folding spontaneous?

A

Gibbs free energy formula helps break it down through enthalpy and entropy. Protein folding is an exothermic reaction, meaning the enthalpy change or delta H is negative. The hydrophobic effect spontaneously encourages nonpolar molecules to clump together. Van der Waal interactions and hydrogen bonding also occur when they hydrophobic tails are close in proximity to each other, resulting in a release in energy of the system (a decrease in enthalpy). Entropy is increased spontaneously, meaning delta S is positive, due to all the interactions occurring in proximity of the molecules, thereby increasing the disorder in the system. The formation of water molecules in hydrogen bonding also contributes to the increase in disorder and entropy.

24
Q

What is the mutation that leads to Sickle Cell Anemia?

A

Glu to Val
(hydrophilic to hydrophobic)

25
Q

How does the mutation contribute to C folding shape in sickle cell anemia?

A

The outside of the protein is now hydrophobic so it interacts with a complementary hydrophobic surface pocket on another hemoglobin molecule. This contributes to the C folding shape that changes the red blood cell shape to more sickle like and leads to blockages in blood flow. Ultimately, the tissues are deprived of oxygen causing sickle cell anemia.

26
Q

What is the Henderson-Hasselbach equation?

A

pH = pka + log ( [A-]/[HA] )

27
Q

Why would a drop in blood pH have an undesirable effect on the proximal histidine’s function?

A

A drop in blood pH would result in a change from the deprotonated form to the protonated form. Because nitrogen is now interacting with the hydrogen atom via a hydrogen bond in the protonated form, the bond to iron would be broken. This would eliminate the ability of proximal histidine to carry oxygen which affects the molecule’s function undesirably

28
Q

Which amino acids have polar side chains + are hydrophilic?

A

Ser, Thr, Cys, Tyr, Asn, Gln

29
Q

Which amino acids have nonpolar side chains + hydrophobic?

A

Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro

30
Q

Which hydrophillic amino acids have R groups with a positive charge? (basic)

A

Lys, Arg, His

31
Q

Which hydrophillic amino acids have R groups with a negative charge? (acidic)

A

Asp and Glu

32
Q

What is Peptide-bond formation?

A

The linking of two amino acids accompanied by the loss of a water molecule

33
Q

What is the primary structure of a protein?

A

amino acid linear sequence

34
Q

What is the secondary structure of protein?

A

regions of regularly repeating conformations of polypeptide chains ( alpha helices + beta sheets)

35
Q

What is the tertiary structure of a protein?

A

describes the shape of the fully folded polypeptide chain

36
Q

What is the quaternary structure of a protein?

A

arrangement of two or more polypeptide chains into a multi subunit molecule

37
Q

What is barter syndrome?

A

Barter syndrome is a group of kidney disorders that disrupts the balance of potassium, sodium, and chloride molecules. It leads to a problem with NaCl reabsorption, salt wasting , which causes an imbalance in ions like potassium and calcium.

38
Q

What protein does KCNJ1 code for? How does this lead to Barter Syndrome?

A

ROMK is a protein responsible for the reabsorption of sodium back into bloodstream

without it, a person struggles to maintain blood pressure and body fluid levels.

39
Q

If the potassium ion channel, ROMK, does not work right, neither does the channel for NaCl.
Why? Explain it.

A

The transport of potassium by ROMK directly affects the ability of another protein, NKC22 to transport ions into the kidney cells as the two are cotransporters. When ROMK isn’t working properly, ions are not transported into the kidney cells. This leads to a buildup of potassium in the cells. In an attempt to retain homeostasis, the cells close the other channels. This blocks the sodium out resulting in a low concentration of sodium and potassium in the blood. As a result, the kidneys have issues with salt reabsorption, salt is not retained, and ions are imbalanced.

40
Q

What does it mean for a molecule to be amphipathic? `

A

A molecule is amphipathic when it has a hydrophilic (polar) head and a hydrophobic (nonpolar) hydrocarbon tail.

41
Q

What is the structure of a phospholipid membrane?

A

hydrophilic head + hydrophobic tail

42
Q

What type of molecules need a channel to cross a membrane?

A

hydrophilic

43
Q

What type of amino acids predominate at the surface of a potassium ion channel in the trans-membrane region?

A

nonpolar amino acids

44
Q

What type of amino acids predominate at the surface of a hemoglobin molecule?

A

polar amino acids

45
Q

Which part of the amino acids do potassium ions interact with in the potassium ion channel?

A

Potassium ions interact with the oxygens of the carbonyl groups of an amino acid in the secondary structure (turns and loops).

BCMB (1 decks)

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