Lecture 1-2 Review

Question 1

Name the 4 types of chemical bonds

Answer 1

Hydrogen interactions, Van Der Walls Interactions, Electrostatic, and covalent bonds

Question 2

For the four chemical bonds, give the bond length and strength

Answer 2

Covalent Bonds - 1.54 Angstroms, 355 kj/mol
Electrostatic - 3 Angstroms, 5.86 kj/mol
Hydrogen Bonds - 1.5/2.6 Angstoms, 4/20 kj/mol
Van Der Waals - n/a, 2-4 kj/mol

Question 3

For both Aldoses and Ketoses, give the names of the triose, pentose, and hexose version of the saccharides

Answer 3

Aldoses: (Glyceraldehyde), (Ribose), (Glucose and Galactose)

Ketoses: (Dihydroxyacetone), (Ribulose), (Fructose)

Question 4

How are polysaccharides synthesized?

Answer 4

Dehydration of the hydroxy bond to form water molecule at either 1-4 linkage, or 1-2 linkage

(Also how many lipids are formed)

Question 5

From Top of the head to the bottom of the tail, name the component sections of a phospholipid

Answer 5

Hydrophilic: Choline Head, Phosphate Group, Glycerol

Hydrophobic: Fatty Acid Tail

Question 6

Name the 4 hierarchal structures of amino chains

Answer 6

Primary - Amino Chains
Secondary Structure: Arranging of chains into alpha helices or beta sheets (usually held together by hydrogen bonds)
Tertiary Structure: Linkage of multiple secondary structures (Can be held together by disulfide bonds)
Quaternary - Multisubunit Proteins

Question 7

Name the components of a polynucleotide, a nucleotide, a nucleoside, each type of nitrogenous base, and the two types of sugars available in a nucelic acid

Answer 7

1. Nucleic Acid of nucleotides joined together by a phosphate bond
2. Nucleotide: Nucleoside + Phosphate Group
3. Nucleoside: Sugar Backbone (pentose) with nitrogenous base attached
4. Pyrimidines: Uracil, Thymine, Cytosine
   Purines: Adenine, Guanine
5. Deoxyribose and Ribose

Question 8

Name the Five Major Properties of Water

Answer 8

1. Polarity
2. Cohesion
3. Range of temperature moderation
4. Expansion upon freezing
5. Versatility as a solvent

Question 9

Define the formula for pH relative to concentration of Hydrogen protons.

Answer 9

pH = -log[H+]

Question 10

What would be the pH of a solution with an [OH-] of 1 * 10^-3

Answer 10

pOH = -log[1*10^-3] = 3

ph = 14 - pOH = 14 - 3 = [11]

Question 11

In order, give the formula for:

1. the equilibrium constant of water (Keq)
2. The ion constant of water (with respect to Keq)
3. The simplified ion constant of water
4. The constant Kw of water
5. The concentration of [OH-] and [H+] at ph = 7

Answer 11

1. Keq = ([H+] * [OH-]) / [H2O]
2. Kw = Keq * [H2O]
3. Kw = [H+] [OH-]
4. 1 * 10^(-14)
5. [OH-] = [H+] = 10^-7

Question 12

Give the formula for

1. Ka
2. pKa,
3. The concentration of [H+] when pKa = pH

Answer 12

1. Ka = ([H+][A-])/[HA]
2. pKa = -log(Ka)
3. [H+] = ([H+][A-]/[HA])

Question 13

What are most buffers composed of?

Answer 13

Weak Acids Mixed with their conjugate bases

Question 14

Give the Henderson-Hasselbach Equation for pH

What is the most important buffer in biological systems?

Answer 14

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

Phosphoric Acid = H2PO4 (2-) (Keeps solution at approximately pH=6.8 (target = 7.4))

Question 15

Give the first two laws of thermodynamics

Answer 15

1. Energy can be neither created nor destroyed. However it can be changed of transferred
2. Every energy transfer or transformation increases the entropy (dispersion of energy) of the universe

(For example, The joining of single strands of DNA into double strands releases heat to compromise for the stabilization of energy)

Question 16

Give the definition of free energy (energy that can do work) in regard to enthalpy, entropy, and temperature

Answer 16

delta(G) = delta(H) - (T*delta(S))

A negative G is a spontaneous reaction

Higher G indicates less stable, but greater capacity for energy (work) release. A Low G indicates high stability and limited capacity for energy (work) release.

Question 17

What are the 3 basic types of work that a cell requires energy for

Answer 17

1. Chemical
2. Transport
3. Mechanical

Most often mediated by the dephosphorylation of ATP (Exergonic Reactions fuel endergonic ones)
ATP = Adenosine Triphosphate (Nucelic Acid with 3 phosphate groups, adenine, and ribose)

Question 18

What are the 3 components of broken down ATP

Answer 18

Hydration of ATP breaks off a phosphate group off the triphosphate leaving the ADP (or AMP), 30-45 kJ of Free Energy, and Inorganic Phosphate (The latter of which does Not capably attach to carbon)

Question 19

Explain how ATP helps convert Glutamic Acid to glutamine (Example of ATP chemical work)

Answer 19

ATP phosphorylates the glutamic acid, making it less stable. At this point, the ammonia (NH3) molecule displaces the phosphorous with itself, forming the resulting glutamine.

Question 20

Give an example of ATP Transport Work, and Mechanical Work

Answer 20

Transport Work - ATP phophorylates transport proteins as a way for them to push molecules and cell components against their gradient (Active Transport)

Mechanical Work - ATP binds noncovalently to motor proteins, then is hydrolyzed off, pushing a vesicle along the cytoskeletal track

Question 21

How is ATP replenished after use?

Answer 21

Converting ADP back into ATP requires energy from other catabolic exergonic reactions (Kreb’s cycle, Glycolysis Path, Oxidation, etc…). Usually performed in the mitochondria

Question 22

How do enzymes help drive a reaction and what are some examples of mechanisms that allow this?

Answer 22

Enzymes lower the activation energy (There is NO change in free energy)
Mechanisms include:
1. Reorienting substrates
2. Straining Substrate bonds
3. Providing a more correct microenvironment
4. Covalently bonding to the substrate (temporary)