What is life? Name some characteristics.
- copy one's self
- organization (compartmentalization)
- convert forms of energy (take in food source--> energy)
- respond to stimuli
- numerous reactions at one time
What is the central dogma?
DNA --transcription (linear nucleic acid)--> NA --translation (linear nucleic acid)--> polypeptide --folding (linear amino acid sequence)-->functional protein (3D structure)
DNA--transcription--> RNA is a focus on the __ aspect of life.
Polypeptide--folding--> protein is more so a __.
biochemical standpoint; very important
Which macromolecules do all the work?
What are the three representations of molecules?
Why are they important?
ball and stick model (best for viewing bonds)
space filling model (best for demonstrating interactions and reactions with other components; more visual in that you can see the spaces particular molecules react in)
line structures (best for viewing cemical atoms involved and their ratios)
In order for molecules to react, they must do what?
come into contact with one another
What is an example of the biochemical unity of organisms?
they share a smiliar protein that has a little cavity for DNA to latch onto
What are the three domains?
What are other important biochemical considerations? Explain.
Time and Space
Time: Even though it takes a while to talk about them, these reactions literally take place in a matter of seconds (millions of reactions)
Space: the distance between two molecules can be the deciding factor as to whether they react or not
Types of bonds
van der Waals
Which bonds are the strongest of the noncovalent ones?
On a scale of energy, which molecule or bond has the most energy? second? third? fourth? fifth? sizth?
3) green light
5) noncovalent bond
What do covalent bonds help do?
What is the energy of one C-C bond?
hold atoms together in a molecule
What helps hold two molecules together?
noncovalent bonds (electrostatic, hydrogen, vdW)
What's so great about noncovalent bonds if they are so weak?
what they lack in strength they make up in number. This helps hold cells together
Electrostatic interactions can be determined by what?
Coloumb's law: E=kq1q2/Dr^2
k= equilibrium constant
q1 and q2= charges of the two atoms involved in the interaction
D= dielectric constant
The dielectric constant is related to what?
the medium in which the molecules are operating
Ionic bonds do what?
hold together the double helix of DNA
Few atoms are __ and participate in 1) __, which is what?
electronegative atoms pulls electron density out of H and causes a partial positive charge to arise in hydrogen, causing it to then be attracted to an adjacent electronegative atom that develops a partial negative charge
Which molecule is the hydrogen bond donor: N--H or N?
When do hydrogen bonds work better?
when the bonds are in a linear direction
What is the energy of a Hydrogen bond?
five to seven kcal/mol
Hydrogen bonds do what due to what?
hold the double helix together due to bases hydrogen bonding to each other
In terms of the bases, how many hydrogen bonds are formed between each base pair?
Adenine -----two hydrogen bonds----- Thymine
Guanine -----three hydrogen bonds-----Cytosine
Why is DNA perfect for replication?
What does DNA do?
because they can be broken and reformed
For bonding, what don't you need? Why not?
You don't need charges, nor do you need polarity.
As atoms get close to each other, electron clouds interact with each other.
At optimal distances, there is an attractive force that helps to develop partial charges.
What are these distances referred to as? What do they do?
van der Waals contacts
they maintain close distances
What organism displays van der Waals interactions and how do they use it to benefit them?
They have hairy structures called seta, which are mostly made of hydrocarbons. With these hydrocarbons, they interact in millions of van der Waals interactions.
How is the adhesive system of a gecko controlled?
Geckos switch it on and off by sliding against a surface and changing direction, thus rupturing the van der Waals interactions
Usually when things are dropped into water, two things can occur. What are they?
they either dissolve in water (polar) or they repel it (nonpolar)
Explain a water molecule.
three atoms, all of which hydrogen bond
- Oxygen pulls electrons towards it, creating an electric dipole
- - oxygen gets a partial negative; hydrogen takes on a partial positive
Explain what happens when nonpolar molecules are dropped into water.
When nonpolar molecules are dropped in water, the water forms cages around them, hoping to hydrogen bond. However, the molecules can't hydrogen bond. And so, they instead disrupt the hydrogen bonds that were formed earlier.
Because water doesn't know what to do, it surrounds the nonpolar molecule. At this point, the nonpolar molecule has a higher surface area exposed to water and the water has less hydrogen bonds formed. This is not a favorable condition. As a result, the nonpolar molecules seek one another out to reduce their surface area; and, water facilitates this by pushing the hydrophobic molecules together, thus maximizing their hydrogen bonding and minimizing the nonpolar molecule's surface area