Chapter 2 Flashcards
What are atoms composed of?
- ) Nucleus: contains neutrons and protons
2. ) Electrons orbiting in the cloud
Atoms Mass#=?
protons + neutrons
Atoms atomic #=?
protons
What are the most abundant biological elements?
Carbon, oxygen, hydrogen, nitrogen
Out of the most abundant biological elements what are their valence’s?
C: 4
O: 2
H: 1
N: 3
Valence:
the amount of electrons that are available to pair to complete an atoms octet.
Ionic vs. Covalent bond?
Ionic: one atom steals an electron from anther causing it to take a negative charge and the other atom to take a positive charge thus drawing the two together
Covalent: atoms share electrons and those electrons orbit the joint atoms
When do ionic bonds typically occur?
When there is a large variance in electronegativity.
When do covalent bonds typically occur?
When there is little to no variance in electronegativity between atoms.
Predictability of the electronegativity of four most common biologically abundant elements:
O»N>C=H
Bond dissociation energy?
energy needed to break a bond
potential energy?
the energy released after breaking a bond that is then transformed to a variety of of forms of energy’s.
Describe the bond dissociation and potential energy as a covalent bond becomes more polar?
bond dissociation energy increases and potential energy decreases.
Describe the bond dissociation and potential energy as a covalent bond becomes more nonpolar?
bond dissociation energy decreases and potential energy increases.
Describe Hydrogen bonds?
- when ever a hydrogen bonds with anther atom typically an oxygen atom. ( this is due to the partial negative charge)
- The differing partial charges will attract other atoms to form weak hydrogen bonds.
What are five interesting properties of water that result from it’s hydrogen bonds?
- ) outstanding solvent for charged/polar particles
- ) nonpolar molecules are unable to make hydrogen bonds, therefore when exposed to water they remain separate.
- ) Water has a high surface tension ( meniscus in a graduated cylinder)
- ) water is more dense as a liquid than a solid
- ) hydrogen bonds are great at absorbing heat and give H2O a high heat of vaporization
PH scale:
The scale showing the amount of dissolved protons in a solution
How to acids and bases differ in proton concentration?
Acids= higher proton concentration Bases= lower proton concentration
What is the equation to determine PH?
pH=-log{H+}
What is the equation to determine the amount of protons in a solution?
{H+}= antilog(-ph)
What does Ph serve to do?
It is important in cells and living systems, as it is required to be balanced to perform biomechanical processes.
What is a buffer?
What is the example mentioned in lecture?
When a buffer is dissolved in solution it serves to reset the imbalance seen.
What is the example of a buffer mentioned in lecture?
CO2 + H2O –>
Potential energy?
Stored energy (chemical)
Kinetic energy?
energy of motion (thermal energy)
What is Gibbs Free energy (g)?
Free energy change associated with a chemical reaction
What is the equation to determine the change in Gibbs free energy?
Derive each unit of the equation
DeltaG= DeltaH - T * DeltaS DeltaG = change in Gibbs Free energy DeltaH = change in enthalpy T = temperature DeltaS = change in entrophy or randomness
What does it mean if DeltaG < 0 ?
What does it mean if DeltaG > 0 ?
- ) the products are at a lower energy state than the reactants, therefore it is exergonic
- ) The products are at a higher energy state than the reactants, therefore is is endergonic
How can we make an educated guess on the outcome of Delta G?
1.) Determine which side ( products or reactants) have more nonpolar bonds, the one with more nonpolar covalent bonds has a higher potential energy.
2.) the side with more nonpolar covalent bonds has a high enthalpy and the side with less a low enthalpy. subtract the products from the reactants and note weather the value is less than or greater than zero.
3.) Next we can look at DeltaS or change in entrophy.
To do this look for which side has larger and more structured molecules. The S will be higher on the side with smaller and less complex molecules, finally subtract the products from the reactants and not if the delta S is less than or greater than zero.
4.) Temperature will always be positive because we are working in units of kelvin, therefor u plug in the values from earlier and see if delta G is less than or greater than zero.
What molecules were present and abundant on the pre-biotic earth?
CO2 ( most abundant source of carbon) H2O, N2, NH3, CH4, and H2
What was the problem with CO2?
The carbon in CO2 isn’t very reactive, because of its polar covalent bonds that have a high dissociation and low potential energy.
What are REDOX reactions?
The process of a carbon become more complex so it becomes more reactive and is able to create more complex molecules.
What does reduced mean?
Gains electrons
What was Stanley Miller known for?
A simulation of the early atmosphere to show carbon in reduced forms is very possible on the probiotic earth.
Where did energy in the atmosphere come from?
Sun
What are Free Radius atoms?
atoms or molecules that contain highly reactive unpaired molecules
what is the probiotic soup model?
- Atmospheric gases dissolve in the water and light energy initiates carbon reduction
- Then hydrogen cyanide/formaldehyde can form.
- These combined with heat can react with heat to form more complex carbon based compounds that were necessary for life on earth.
What is the surface metabolism model?
- The focus is on the geologically dynamic vents located in the bottom of the ocean
- The vents are hot and high in pressure, and their insides are very rigid and full of crevice’s.
- molecules gather in these crevice’s and obv. increase in concentration.
- Increased concentration combined with the environmental factors creates carbon reduction which allows for it form more complex compounds
What are the six function groups commonly attached to carbon atoms?
Amino Carboxyl Carbonyl Hydroxyl Phosphate Sulfhydryl
