Chapter 1- Biochemistry is an evolving science

Question 1

What is the natural solvent in the body?

Answer 1

Water

Question 2

2 main properties of water

Answer 2

1. Water is a polar molecule

2. Water can form strong intermolecular bonds with other water molecules

Question 3

Why is water a polar molecule?

Answer 3

Charge is not evenly distributed. Water has a bent shape (not 180 degrees), with the large oxygen atom in the middle. Oxygen is much more electronegative and pulls the electron density away from the hydrogens. It has a partial negative charge. Therefore, the dipole moments point toward the oxygen from the hydrogen

Question 4

Hydrogen bond

Answer 4

A hydrogen bond is a very strong intermolecular bond due to the size of the H atom- the nuclei of the 2 atoms can get closer to each other. A hydrogen atom is bonding with some sort of partially negative charge, which is oxygen in the case of water (can also be nitrogen).

Question 5

How do water molecules bond with other water molecules?

Answer 5

Water molecules form hydrogen bonds with each other. The partially negative oxygen on one molecule will be attracted to the partially positive hydrogen on another molecule.

Question 6

As distance between two atoms decreases, the force of the bond

Answer 6

Increases

Question 7

Hydrophobic effect

Answer 7

When two nonpolar molecules are added to water at once, the water molecules will form a cage around both of the nonpolar molecules. This is not favorable, so the two nonpolar molecules will aggregate (clump together). The nonpolar molecules will bond with each other. This decreases the amount of surface area around the entire nonpolar molecule, which decreases the number of trapped water molecules and therefore increases the number of hydrogen bonds the water molecules can make.

Question 8

What happens if a single nonpolar molecule is put in water?

Answer 8

Water molecules will form a “cage” around the nonpolar molecule. This is not a stabilizing effect because the water molecules will be “trapped” around the nonpolar molecule and will not be able to interact favorably with other water molecules. Limits the amount of hydrogen bonds that can be formed between the water molecules

Question 9

What happens if we put a polar molecule in water?

Answer 9

If we put a polar substance into water molecules (like sodium chloride) the molecule will separate (the ionic bond will break). Bonds form between sodium and water and chloride and water. Multiple bonds can form between water and each ion- the reaction is favorable because we form many hydrogen bonds in place of the ionic bond that was broken. The water molecule orients so the oxygen is in close proximity with the sodium (which lost an electron- gets a positive charge). Hydrogen is in close proximity with chloride, which gained an electron and now has a negative charge.

Question 10

Are ionic bonds polar or nonpolar?

Answer 10

Polar- ionic bonds are basically just unequal distributions of charge

Question 11

Hydrophobic interactions

Answer 11

The interactions between the nonpolar molecules and water- different from the hydrophobic effect since the effect describes interactions between the nonpolar molecules in a polar solvent.

Question 12

Electrostatic force

Answer 12

Attractive or repulsive forces between charged groups. Opposite charges will attract each other, while like charges will repel.

Question 13

Intramolecular bonds

Answer 13

Hold the atoms together within a given molecule. They are stronger on average than intermolecular bonds

Question 14

Intermolecular bonds

Answer 14

Hold together the atoms of two different molecules.

Question 15

Covalent bond

Answer 15

Bond in which we have the sharing of electrons- these are the strongest bonds, with double covalent bonds being even stronger

Question 16

Coulomb’s equation

Answer 16

Gives us the magnitude of electrostatic force. D is the dielectric constant. As D decreases, the strength of electrostatic interactions increase.

Question 17

Nonpolar covalent bonds

Answer 17

Occurs when electrons are shared equally. Electronegativity is equal, like bonds between two of the same atom (bond between 2 carbons).

Question 18

Polar covalent bonds

Answer 18

Occurs when one atom attracts electron density more strongly than the other. This is a bond where one atom is partially positive and one is partially negative, like the bond between oxygen and carbon. Oxygen is more electronegative and pulls the electrons toward it, so it gets the partial negative charge.

Question 19

Double and triple covalent bonds

Answer 19

A double or triple bond means that there is more electron density being shared between two atoms. This brings the atoms closer together. Because the atoms are closer together, the force between them is stronger. This is why double and triple bonds are stronger than single bonds.

Question 20

Ionic bonds

Answer 20

Occurs in molecules like sodium chloride. One atom (chloride in this case) is so electronegative that it completely pulls an electron off of the other atom. This is a full separation of charge (one atom has a completely positive charge, and the other a completely negative charge), so the atoms are held together.

Question 21

Types of intramolecular bonds (3)

Answer 21

1. Polar covalent
2. Nonpolar covalent
3. Ionic

Question 22

Types of intermolecular bonds (2)

Answer 22

1. Hydrogen

2. Van der waals forces

Question 23

Hydrogen bond acceptor

Answer 23

The group with the partial negative charge

Question 24

Hydrogen bond donor

Answer 24

The group with the partial positive charge

Question 25

Van der waals forces

Answer 25

Electron density fluctuates/changes over time. A bond between two carbon atoms would be symmetrical and not have a dipole moment. However, at any moment in time, the electron density might be surrounding one carbon atom or another carbon atom since the electrons are continuously fluctuating. In these situations, an instantaneous dipole moment would occur. This would mean that the carbon with more electron density temporarily has a partial negative charge and the other carbon has a partial positive charge. The partial charges fluctuate over time, and the carbons can switch their partial charges. These are the weakest forces because they only exist for a moment in time.

Question 26

All reactions in biochemistry obey which 2 laws?

Answer 26

The first and second law of thermodynamics

Question 27

System

Answer 27

A region of space that contains all of the atoms and molecules that we’re studying. Everything else (outside of the system) is called the surroundings. Adding the molecules in our system and the molecules in our surroundings will give us the molecules of our universe.

Question 28

First law of thermodynamics

Answer 28

The law states that the energy of our system and the energy of our surroundings adds to equal the energy of the universe, which is always constant. This means that energy can be transformed, but not created or destroyed. For example, a marker held above the ground has gravitational potential energy, but this energy decreases as it falls. The potential energy is converted to kinetic energy

Question 29

Entropy

Answer 29

The amount of randomness and disorder in a system

Question 30

Second law of thermodynamics

Answer 30

The law states that every time a physical/chemical reaction takes place, the change in entropy of the universe is always positive (the entropy of the universe always increases). The entropy of a system can be negative, but the net change in entropy of the universe is always greater than 0. A system will always try to become as random as possible.

Question 31

What are examples of a system becoming as random as possible?

Answer 31

1. Molecules concentrated on one side of a system will try to spread out if possible
2. Energy will always try to disperse throughout all of the space where it exists
3. Energy always travels from a high amount to a low amount until it reaches equilibrium (both sides have equal energy)- this represents the highest amount of entropy

Question 32

How does the second law of thermodynamics describe the hydrophobic effect?

Answer 32

The aggregation of nonpolar molecules in water increases the entropy of the system. This decreases the amount of water molecules on the surface- some of the water molecules will leave and will be moving around randomly in solution, which is consistent with the law. The water molecules are now more disordered than before, making the hydrophobic effect advantageous.

Question 33

Gibbs free energy

Answer 33

The Gibbs free energy equation measures the overall change in energy of the system (delta G). If delta G is negative, that indicates a spontaneous reaction that increases the entropy of the universe. If positive, the reaction is not spontaneous and will not take place naturally

Question 34

In biological reactions, which 4 factors play a role in determining the reaction pathway and product structure?

Answer 34

1. Intermolecular bonds (and hydrophobic interactions)
2. The solvent of the reaction
3. Thermodynamics
4. pH of the solution can also influence the reaction

Question 35

Structure of DNA

Answer 35

The outside of the DNA has the phosphate groups and the carbon backbone, and the deoxyribose sugars. On the inside, we have the bases that pair with each other

Question 36

How do intermolecular forces drive the formation of the double helix?

Answer 36

DNA is floating around in water, which predominates in the nucleus and is a polar molecule. The bases are primarily nonpolar and won’t want to interact with the polar solvent. The double helix structure puts the nonpolar bases inside of the double helix so they’re not near the polar solvent (hydrophobic effect), making the structure more stable.

Question 37

Which unfavorable reaction occurs in DNA?

Answer 37

The unfavorable reaction occurs between the phosphate groups. Phosphate groups have negative charges, and the multiple like charges will repel each other. At body temperature, the attractive forces overpower the repulsive forces, so that’s why the structure remains

Question 38

How do the properties of water (the solvent) affect the structure of the DNA molecule?

Answer 38

The hydrogens on the water molecules interact with the oxygens on the phosphate groups, forming hydrogen bonds. This has a stabilizing effect and favors the double helix formation

Question 39

What happens to entropy as DNA becomes a double helix?

Answer 39

As the DNA becomes a double helix, the entropy actually becomes more negative due to the increased order in the system. A lot of heat is released into the surroundings, which increases the entropy of the surroundings by a greater amount than the decrease in the entropy of the system. Therefore, this reaction is favorable

Question 40

Acid base reaction

Answer 40

When a hydrogen ion is exchanged between 2 molecules. The acid donates a hydrogen, breaking a bond. The base accepts the hydrogen due to its (base’s) lone pair of electrons and forms a covalent bond

Question 41

What is usually the solvent for acid base reactions?

Answer 41

Acid base reactions usually take place in water due to all of the water in our bodies

Question 42

pH

Answer 42

We use pH to determine the concentration of the solution. Equal to negative log of the hydrogen ion concentration in the solution. If pH=7, we can calculate the concentration: 10 X 10 ^-7.

Question 43

Acidic solutions

Answer 43

pH is lower than 7. In acidic solutions, the concentration of hydrogen ions is greater than the concentration of hydroxide ions

Question 44

Basic solutions

Answer 44

pH is greater than 7. In basic solutions, the concentration of hydrogen ions is less than the concentration of hydroxide ions.

Question 45

At what pH does DNA start to dissociate?

Answer 45

As we approach 9, a small change in pH results in a large change in the amount of DNA molecules that dissociate and are no longer in their double helix form- percentage of DNA molecules in their double helix form decrease. By the time we get past a pH of 10, less than 10% of DNA molecules are in their double helix form

Question 46

Ka

Answer 46

Acid dissociation constant- a ratio between the concentration of the products (H and A ions) and the concentration of the reactants (HA). The greater the Ka, the stronger the acid. The greater the Ka, the greater the numerator is and the greater the number of products we make- if we form more products, that means the acid is a stronger acid, since more hydrogen ion is produced

Question 47

pKa

Answer 47

Used more commonly than Ka as a dissociation constant. It is the negative log of the Ka value. The greater the Ka, the smaller the pKa, which means that stronger acids have lower pKa values (they will be more likely to donate hydrogen ions).

Question 48

When can DNA bases act as acids?

Answer 48

The hydrogen bonded to the nitrogen in guanine can act as an acid- at a certain pH, it will begin to dissociate. If the pH is high enough- guanine will become a good acid and readily dissociate. This is a problem because the hydrogen ion will interact with another base to form a hydrogen bond, and hydrogen bonds hold the bases together.

Question 49

Why is it bad for DNA bases to be deprotonated as the pH becomes more basic?

Answer 49

This is bad because the H in guanine participates in a hydrogen bond with the N in cytosine- removing the H disrupts the hydrogen bond between the bases. Creates 2 like charges that repel each other, causing the DNA bases to dissociate

Question 50

In general, what does increasing the pH do to hydrogen bonds?

Answer 50

Increasing the pH decreases the amount of hydrogen bonds, destabilizing the double helix structure. This is why the cells of our body use so much energy trying to maintain a constant pH. Changing pH affects all of the biological processes in the cell

Question 51

In general, what does decreasing the pH do to hydrogen bonds?

Answer 51

The atoms involved in forming hydrogen bonds will be protonated, disrupting the bonding and destabilizing the structure.

Question 52

Buffer systems definition

Answer 52

For the body and the cells to function normally, we need a body system to prevent drastic pH changes. In a buffer system, we have water as a solvent, but we also have a certain concentration of an acid and an equal concentration of its conjugate base. If an acid base reaction takes place, the conjugate base can interact and consume the H cations to decrease the amount. This creates a gradual change in pH instead of a drastic one

Question 53

Without a buffer system in the nucleus, what happens if you add H cations to pure water?

Answer 53

If we add H cations to the nucleus, we would have an acid base reactions in the nucleus- pH drops drastically very quickly. Therefore, pure water is not a good system to prevent these drastic changes in pH. If the cells of the body contained pure water, acid base reactions would end up destroying many biomolecules

Question 54

In a buffer system, why does the pH change gradually?

Answer 54

The CB concentration is exactly the same as the acid concentration (HA)= (A-). CB will react with added H+ ions, the pH doesn’t change as drastically

Question 55

Henderson-Hasselbach equation

Answer 55

Tells us that the pH of our solution that contains the buffered system is equal to the pKa value of that particular acid that is used in that buffered system plus the log of the ratio of the conjugate base to its acid

Question 56

Why do we want equal concentrations of HA (acid) and A- (CB) in a buffer system?

Answer 56

The point of the curve with the flattest slope is the point where the buffer system has the greatest ability to prevent the change in pH from taking place. Example system- the best pH for the system to resist change in pH is 4.75, and the pKa of acetic acid is 4.75. This is not a coincidence- using the HH equation, pH is only equal to pKa when the concentration of the acid and CB is equal. Then, the ratio equals 1, the log equals 0, and pH and pKa are mathematically equal.

Question 57

Buffers function best at the pH value corresponding to

Answer 57

The pKa of the acid. If we have a solution that we want to remain at a specific pH, we have to find an acid to serve as a buffered system that has a pKa value that is equivalent to that specific pH value

Question 58

D configuration

Answer 58

R configuration in a chiral molecule

Question 59

L configuration

Answer 59

S configuration in a chiral molecule