Lecture 1-2 Review Flashcards
Name the 4 types of chemical bonds
Hydrogen interactions, Van Der Walls Interactions, Electrostatic, and covalent bonds
For the four chemical bonds, give the bond length and strength
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
For both Aldoses and Ketoses, give the names of the triose, pentose, and hexose version of the saccharides
Aldoses: (Glyceraldehyde), (Ribose), (Glucose and Galactose)
Ketoses: (Dihydroxyacetone), (Ribulose), (Fructose)
How are polysaccharides synthesized?
Dehydration of the hydroxy bond to form water molecule at either 1-4 linkage, or 1-2 linkage
(Also how many lipids are formed)
From Top of the head to the bottom of the tail, name the component sections of a phospholipid
Hydrophilic: Choline Head, Phosphate Group, Glycerol
Hydrophobic: Fatty Acid Tail
Name the 4 hierarchal structures of amino chains
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
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
- Nucleic Acid of nucleotides joined together by a phosphate bond
- Nucleotide: Nucleoside + Phosphate Group
- Nucleoside: Sugar Backbone (pentose) with nitrogenous base attached
- Pyrimidines: Uracil, Thymine, Cytosine
Purines: Adenine, Guanine - Deoxyribose and Ribose
Name the Five Major Properties of Water
- Polarity
- Cohesion
- Range of temperature moderation
- Expansion upon freezing
- Versatility as a solvent
Define the formula for pH relative to concentration of Hydrogen protons.
pH = -log[H+]
What would be the pH of a solution with an [OH-] of 1 * 10^-3
pOH = -log[1*10^-3] = 3
ph = 14 - pOH = 14 - 3 = [11]
In order, give the formula for:
- the equilibrium constant of water (Keq)
- The ion constant of water (with respect to Keq)
- The simplified ion constant of water
- The constant Kw of water
- The concentration of [OH-] and [H+] at ph = 7
- Keq = ([H+] * [OH-]) / [H2O]
- Kw = Keq * [H2O]
- Kw = [H+] [OH-]
- 1 * 10^(-14)
- [OH-] = [H+] = 10^-7
Give the formula for
- Ka
- pKa,
- The concentration of [H+] when pKa = pH
- Ka = ([H+][A-])/[HA]
- pKa = -log(Ka)
- [H+] = ([H+][A-]/[HA])
What are most buffers composed of?
Weak Acids Mixed with their conjugate bases
Give the Henderson-Hasselbach Equation for pH
What is the most important buffer in biological systems?
pH = pKa + log([A-]/[HA])
Phosphoric Acid = H2PO4 (2-) (Keeps solution at approximately pH=6.8 (target = 7.4))
Give the first two laws of thermodynamics
- Energy can be neither created nor destroyed. However it can be changed of transferred
- 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)
Give the definition of free energy (energy that can do work) in regard to enthalpy, entropy, and temperature
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.
What are the 3 basic types of work that a cell requires energy for
- Chemical
- Transport
- 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)
What are the 3 components of broken down ATP
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)
Explain how ATP helps convert Glutamic Acid to glutamine (Example of ATP chemical work)
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.
Give an example of ATP Transport Work, and Mechanical Work
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
How is ATP replenished after use?
Converting ADP back into ATP requires energy from other catabolic exergonic reactions (Kreb’s cycle, Glycolysis Path, Oxidation, etc…). Usually performed in the mitochondria
How do enzymes help drive a reaction and what are some examples of mechanisms that allow this?
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)
