Organic Molecules + Some Basic Review

Reflecting back on the week, I discovered something: I am still really confused on macromolecules. So, I decided to really focus in on identifying the four different macromolecules, and here are summaries of each.

  • DNA is found in the nucleus
  • There are 4 different types of macromolecules:
    • Nucleic Acids
      • Essentially DNA and RNA
      • Nucleotides are the building blocks: They are made up of a sugar base, a nitrogenous base and a phosphate group
      • rna v dna.png
        The backbone of the RNA/DNA is a combination of a phosphate and sugar, and then the phosphate group is attached to the backbone
      • They carry genetic material and carry it generation to generation
      • Functions: 
        • store and transfer genetic information
        • use the genetic information to direct the synthesis of a new protein
        • DNA controls the synthesis of RNA
    • Proteins
      • Amino acids are the building blocks of proteins
        • There are 20 known amino acids
        • amino-acid-structure
          The basic structure of an Amino Acid
      • R-groups are the thing that differentiates nucleic acid from other amino acids
      • Functions: 
        • do most of the work in cells and are required for the structure, function, and regulation of the body’s tissues and organs
    • Lipids
      • One monomer
      • Make up all the cell membranes
      • Have polarity: generally nonpolar, but some parts can be polar
      • Lipid.png
        They all have the ‘hydrocarbon tail’ in common– making them nonpolar. Therefore, they don’t mix well with water (hydrophobic)
      • Unsaturated fat: has a double bond, or more then one.
      • Saturated: no double bond
      • Trans-fat: hydrogen has been added to the fat or is naturally occurring
      • Functions:
        • fatty acids represent an important source of energy, particularly for the purposes of long-term storage
        • Cholesterol, a lipid, can be used to make many other compounds in the body, such as steroid hormones
        • Key components of the membranes that surround cells
    • Carbohydrates
      • Sugar is the monomers of carbohydrates
        • Glucose– put them together to create amylose
      • Gives us energy and also structure
        • cellulose in plants
      • Functions: 
        • the preferred source of energy for most of the tissues in the body, including the nervous system and the heart
        • Carbohydrates from the diet are converted into glucose, which can either be immediately used as a source of energy or stored in the form of glycogen
        • Also help maintain proper digestive health
  • Monomers: the small building blocks that make up biological molecules/ polymers
  • Dehydration Synthesis: 
    • Lose a water
      • A covalent/ peptide bond is formed
  • Hydrolysis:
    • Add a water, which breaks the monomers apart

hydrolysis.png

  • Hydrophilic: capable of interacting with water through hydrogen bonding. Hydrophilic groups generally have polar groups which enable them to bond easily with water/dissolve into them.
  • Hydrophobic: Insoluble with water, repels water. EX: Oil is hydrophobic
    • How I will remember this: hydrophobia is the fear of water, so hydrophobic is staying away from water. Phobia is to stay away from something/fearing it.
  • What does it mean to be polar or non-polar?
    • Polar: Chemical bonding is the result of either covalent or ionic bonding. Normally, an atom has an even distribution of electrons in the orbits or shells, but if more end up on one side that the other in a molecule, there can be a resulting electrical field in that area, creating the polar effect.
    • Screen Shot 2016-11-05 at 1.20.28 PM.png
      WATER IS A POLAR MOLECULE: the hydrogen atoms make it positive on one end, making the molecule negative on the other side.
    • Non-polar: one in which the electrons are distributed more symmetrically and thus does not have an abundance of charges at the opposite sides. The charges all cancel out each other

      Screen Shot 2016-11-05 at 1.24.10 PM.png
      CO2 is an example of a non-polar molecule

Some questions about organic molecules:

In the Bozeman video, he talks a lot about directionality. What does he mean? What is meant when he says that each macromolecule has a different directionality?

Are peptide bonds and covalent bonds the same thing?

So, besides all that review, we started a protein chemistry lab on Thursday. The main thing I took away from this was how pH and temperature affect the chemical bonds of a protein. When we put the egg into the boiling water (poached egg yum), we immediately saw a change happening to the structure of the egg. What was really happening? Basically, the egg was coagulating. The proteins that bond the egg together are very easily disturbed to changes in temperature or pH, causing the protein molecules to bond together into a solid mass (aka to coagulate). When the egg was being heated, the increased energy of all the molecules in the egg broke some of the bonds that keep the albumen proteins in their shape, causing the individual protein molecules to unfold. As the temperature goes up, the proteins unfold more, bumping into each other more and thus bonding increases. This is also the process of denaturing as well: denaturing is when a protein loses its 3-D shape an unravels back into a long chain.

After finishing the lab, my lab group started filling out the questions, and I came across something I wasn’t familiar with; secondary and tertiary structures of a protein. What are these? How do they behave differently compared to a primary structure? And what even defines a primary structure?

Side Note:

Mini review of Standard Deviation and Standard Error of the Mean:

The differences between Standard Deviation and Standard Error:

Standard Deviation: The measure of how spread out numbers are.

  • How much the values differ from each other
  • As more data is collected, the more accurate the standard deviation is/ the data in general
  • For data with a normal distribution, about 95% of individuals will have values within 2 standard deviations of the mean, the other 5% being equally scattered above and below these limits
  • A low standard deviation indicates that the data points tend to be close to the mean of the set, while a high standard deviation indicates that the data points are spread out over a wider range of values
  • the standard deviation will not tend to change as the size of sample is increased
standard deviation.png
Each band represents the width of one standard deviation

Standard Error:

  • how precise the true mean of the population is. It takes into account both the value of the standard deviation and the sample size
  • The standard error is always smaller then the standard deviation of the sample size.
  • The relationship of standard error to standard deviation is as follows:
    • SE = SD/√(sample size)
  • The standard error falls as the sample size increases, as the extent of chance variation is reduced
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