Chapter 2 Biochem

Question 1

Molecules joined together form larger units called ____?

Answer 1

Polymers or macromolecules

Question 2

What enviroment is crucial for molecular interactions within living organisms?

Answer 2

Aqueous enviroment because cells are 70-80% water.

Question 3

What is atomic number?

Answer 3

Number of protons

Question 4

What is atomic mass?

Answer 4

Number of protons + electrons

Question 5

What determines the atom’s interaction with others?

Answer 5

Arrangement of electrons.

Question 6

How many electrons are in the 1st - 4th shells?

Answer 6

1st - 2
2nd - 8
3rd - 8
4th - 18

Question 7

What is the most stable and chemically unreactive arrangement of electrons?

Answer 7

Outermost shell to be filled.

Question 8

How does atoms become molecules?

Answer 8

When unfilled (chemically active) outer shells share electrons.

Question 9

What is a single and double bond?

Answer 9

Single - sharing one pair of electrons
Double - sharing two pairs of electrons

Question 10

What types of bonds are very stable?

Answer 10

Covalent bonds.

Question 11

What are peptide bonds?

Answer 11

Covalent bonds that form between amino acids to form polypeptides (chains) and proteins.

Question 12

What structure (shape) is the peptide bond?

Answer 12

Planar - crucial for protein structure and function.

Question 13

Shape of a molecule is determined by what?

Answer 13

The distribution of electrons.

Question 14

What structure does 4 single bonds between carbon form?

Answer 14

Tetrahedron - equally spaced from aother (methane)

Question 15

Discuss the movement of atoms between single and double bonds.

Answer 15

Single - rotate freely.
Double - rotation restricted around bond, other bonds in single plane (ethene).

Question 16

What is the “van der Waals radius”?

Answer 16

Half the distance between the nuclei of two identical, non-bonded, closest-approach atoms, representing the size of an atom when it’s not chemically bound.

Question 17

Describe the interactions between atoms at different distances.

Answer 17

Closer than van der Waals radii > strongly repulsed.
Close enough (van der Waals radius) > weakly attracted.
Very far > no energetic interaction.

Question 17

Describe electrons being shared unequally within a covalent bond.

Answer 17

Greater share of electron > electronegative = negatively charged δ-
Lesser share of electron > electropositive = positively charged δ+

Question 17

What is “dipole”?

Answer 17

AKA separation of charge.
A pair of electric charges or magnetic poles, of equal magnitude but of opposite sign or polarity, separated by a small distance.

Question 18

What are Polar molecules?

Answer 18

Covalent bonds with a dipole.
Hydrophilic - interact favorably with water.

Question 19

What are Non-polar molecules?

Answer 19

Equal sharing of electrons.
Hydrophobic -prefer to associate with one another (fatty-acids).

Question 20

What is Ionization?

Answer 20

Atoms gain or lose electrons entirely, becoming fully electrostatically charged, due to energetic preference for a completely filled outer shell.

Question 21

What is a negative and positive ion called?

Answer 21

Negative:Anion
Positive: Cation

Question 22

Whar do charged ions interacting with each other form?

Answer 22

Salts.

Question 23

What are the 2 properties of water?

Answer 23

1. Ability to form hydrogen bonds. 2. Ability to be ionized.

Question 24

When water is ionized, which 2 ions are formed?

Answer 24

Hydroxide (OH−) or hydronium (H3O+).

Question 25

What is the concentration of Hydroxide (OH−) or hydronium (H3O+)?

Answer 25

10^-7M

Question 26

Which ions affect biological reactions?

Answer 26

H+ ions

Question 27

What are acids and bases?

Answer 27

Acid: release H+ when dissolved in solution Base: absorb H+ when dissolved in solution

Question 28

What is pH?

Answer 28

The measure of H+ ions in a solution. pH = -log[H+]

Question 29

What are covalent bonds?

Answer 29

Sharing of electrons b/w atoms to form molecules.

Question 30

What are the important roles of non-covalent bonds?

Answer 30

Weaker than covalent, but important for structure and stabilization. Weaker bonds allow for bonds to be easily broken and formed = flexibility for function (protein binding to DNA, muscle contraction, signaling)

Question 31

What are the 3 principle types?

Answer 31

1. Salt bridges: ionic interactions b/w charged atoms. 2. Hydrogen bonds: interactions b/w polar atoms with partial charges (dipoles). 3. Van der Waals: weak attractions b/w atoms at a certain distance.

Question 32

What is a hydrogen bond?

Answer 32

Electrostatic interactions b/w + end of dipole and - charge of another. Consists of a hydrogen donor (N/O - H) and hydrogen acceptor (N/O).

Question 33

What is the + end on a hydrogen?

Answer 33

Electronegative atom (O and N)

Question 33

When is the energy of a hydrogen bond greatest?

Answer 33

When the 3 atoms involved lie in a straight line.

Question 34

What causes the interaction strength to weaken? (hydrogen bond)

Answer 34

When the angles increase.

Question 35

True/False: Van der Waals interactions only occur between charged atoms.

Answer 35

False. All atoms attract each other (charged or not).

Question 36

Describe transient dipoles.

Answer 36

Created due to electron movements around atoms. (Assymetric electron distribution). If such an atom is close to another, it induces a dipole in the 2nd atom. The weak charges attract one another and stabilize the dipoles somewhat.

Question 37

What is the properties of water H2O? (2.2)

Answer 37

1. polar molcule (bent) 2. highly cohesive - high dielectric constant 80 - interact with molecules through hydrogen bond and ionic interaction.

Question 38

Explain the result of salt bridges in water.

Answer 38

Absence of water: strong and stable Presence of water: weakend by polar water molecules that interact with the charges (dissolves table salt)

Question 39

What does an aqueous enviroment affect? (2)

Answer 39

1. Strength of interactions b/w molecules 2. Types of interactions that can occur

Question 40

How do non-polar and polar molecules interact with water?

Answer 40

Non-polar: hydrophobic = not favorably Polar: hydrophilic = interact

Question 41

Describe hydrophobic and hydrophilic interactions.

Answer 41

> Hydrophobic interactions drive molecular folding & the regions associate with one another and exclude water (partitioning). > Hydrophilic regions are located on outside surface of molecule where it can interact with water.

Question 42

What is needed for the stabilization of macromolecule binding?

Answer 42

Enzymes must precisely match their substrates in order to perform their functions.

Question 43

What determines the strength of interaction?

Answer 43

1. Shape 2. Chemical nature of of contacting surface (specificity & non-covalent)